Starting phenix.real_space_refine on Tue Feb 3 21:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wsw_66208/02_2026/9wsw_66208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wsw_66208/02_2026/9wsw_66208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wsw_66208/02_2026/9wsw_66208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wsw_66208/02_2026/9wsw_66208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wsw_66208/02_2026/9wsw_66208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wsw_66208/02_2026/9wsw_66208.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 4553 2.51 5 N 1215 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7134 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1828 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2269 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Classifications: {'peptide': 4} Link IDs: {'PTRANS': 1, 'TRANS': 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 7134 At special positions: 0 Unit cell: (87.42, 99.51, 129.27, 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 58 16.00 O 1308 8.00 N 1215 7.00 C 4553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 222.5 milliseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 47.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.588A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.474A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.107A pdb=" N ILE A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.296A pdb=" N ARG A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.916A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 66 through 96 Processing helix chain 'R' and resid 101 through 120 Processing helix chain 'R' and resid 120 through 131 removed outlier: 3.775A pdb=" N GLN R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 171 removed outlier: 4.130A pdb=" N LEU R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 3.510A pdb=" N LEU R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 205 removed outlier: 4.075A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 224 through 241 removed outlier: 3.532A pdb=" N TRP R 228 " --> pdb=" O PRO R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 Processing helix chain 'R' and resid 268 through 306 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 337 removed outlier: 3.988A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 345 removed outlier: 3.506A pdb=" N ARG R 345 " --> pdb=" O GLU R 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.629A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.457A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.624A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.201A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.601A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.772A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.593A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.692A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 206 through 210 removed outlier: 3.565A pdb=" N ASP R 216 " --> pdb=" O LYS R 209 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1161 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: 1.18 Time building geometry restraints manager: 0.85 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: 1884 1.33 - 1.45: 1339 1.45 - 1.57: 3966 1.57 - 1.69: 0 1.69 - 1.82: 83 Bond restraints: 7272 Sorted by residual: bond pdb=" C ILE R 308 " pdb=" N PRO R 309 " ideal model delta sigma weight residual 1.332 1.370 -0.038 1.34e-02 5.57e+03 8.00e+00 bond pdb=" C TYR R 75 " pdb=" O TYR R 75 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.17e-02 7.31e+03 4.25e+00 bond pdb=" CA ILE R 308 " pdb=" C ILE R 308 " ideal model delta sigma weight residual 1.523 1.541 -0.018 8.80e-03 1.29e+04 4.00e+00 bond pdb=" N MET R 99 " pdb=" CA MET R 99 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.70e+00 bond pdb=" C CYS R 79 " pdb=" O CYS R 79 " ideal model delta sigma weight residual 1.237 1.215 0.022 1.17e-02 7.31e+03 3.53e+00 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 9585 1.53 - 3.06: 216 3.06 - 4.60: 32 4.60 - 6.13: 12 6.13 - 7.66: 5 Bond angle restraints: 9850 Sorted by residual: angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.14 116.08 -6.94 1.49e+00 4.50e-01 2.17e+01 angle pdb=" C ILE R 308 " pdb=" N PRO R 309 " pdb=" CA PRO R 309 " ideal model delta sigma weight residual 119.78 115.19 4.59 1.03e+00 9.43e-01 1.98e+01 angle pdb=" N ILE R 308 " pdb=" CA ILE R 308 " pdb=" C ILE R 308 " ideal model delta sigma weight residual 107.89 112.06 -4.17 1.09e+00 8.42e-01 1.46e+01 angle pdb=" N LEU R 74 " pdb=" CA LEU R 74 " pdb=" C LEU R 74 " ideal model delta sigma weight residual 111.28 107.89 3.39 1.09e+00 8.42e-01 9.65e+00 angle pdb=" N PHE A 215 " pdb=" CA PHE A 215 " pdb=" C PHE A 215 " ideal model delta sigma weight residual 112.92 109.17 3.75 1.23e+00 6.61e-01 9.27e+00 ... (remaining 9845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4049 17.88 - 35.77: 241 35.77 - 53.65: 43 53.65 - 71.53: 6 71.53 - 89.42: 5 Dihedral angle restraints: 4344 sinusoidal: 1706 harmonic: 2638 Sorted by residual: dihedral pdb=" CB CYS R 140 " pdb=" SG CYS R 140 " pdb=" SG CYS R 217 " pdb=" CB CYS R 217 " ideal model delta sinusoidal sigma weight residual 93.00 -177.58 -89.42 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 4341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 708 0.035 - 0.070: 291 0.070 - 0.104: 92 0.104 - 0.139: 38 0.139 - 0.174: 9 Chirality restraints: 1138 Sorted by residual: chirality pdb=" CA LEU R 139 " pdb=" N LEU R 139 " pdb=" C LEU R 139 " pdb=" CB LEU R 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU R 139 " pdb=" CB LEU R 139 " pdb=" CD1 LEU R 139 " pdb=" CD2 LEU R 139 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1135 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 98 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.05e+00 pdb=" C LYS R 98 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS R 98 " 0.017 2.00e-02 2.50e+03 pdb=" N MET R 99 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 27 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 27 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 27 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 28 " -0.010 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 784 2.75 - 3.29: 7095 3.29 - 3.82: 12193 3.82 - 4.36: 14360 4.36 - 4.90: 25102 Nonbonded interactions: 59534 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 186 " pdb=" NZ LYS A 197 " model vdw 2.239 3.120 nonbonded pdb=" OG SER A 263 " pdb=" O GLU A 318 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.260 3.040 nonbonded pdb=" NH1 ARG R 277 " pdb=" OE2 GLU R 341 " model vdw 2.275 3.120 ... (remaining 59529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.890 Find NCS groups from input model: 0.020 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:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 0.003 0.101 7274 Z= 0.207 Angle : 0.580 7.658 9852 Z= 0.336 Chirality : 0.046 0.174 1138 Planarity : 0.004 0.048 1234 Dihedral : 12.139 89.010 2629 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 889 helix: 1.84 (0.26), residues: 400 sheet: 0.47 (0.40), residues: 180 loop : -0.57 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.011 0.001 TYR B 59 PHE 0.011 0.001 PHE R 178 TRP 0.020 0.002 TRP R 228 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7272) covalent geometry : angle 0.57981 ( 9850) SS BOND : bond 0.00086 ( 1) SS BOND : angle 1.46518 ( 2) hydrogen bonds : bond 0.15765 ( 401) hydrogen bonds : angle 6.45649 ( 1161) Misc. bond : bond 0.10059 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8023 (mt-10) REVERT: G 15 LEU cc_start: 0.8202 (tt) cc_final: 0.7950 (tp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.6525 time to fit residues: 110.3392 Evaluate side-chains 113 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 75 GLN B 176 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135383 restraints weight = 8125.138| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.74 r_work: 0.3388 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7274 Z= 0.140 Angle : 0.547 6.479 9852 Z= 0.293 Chirality : 0.043 0.143 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.325 18.319 974 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.55 % Allowed : 12.48 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.28), residues: 889 helix: 1.87 (0.26), residues: 401 sheet: 0.45 (0.38), residues: 182 loop : -0.70 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.014 0.001 TYR B 105 PHE 0.019 0.001 PHE R 84 TRP 0.015 0.002 TRP R 228 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7272) covalent geometry : angle 0.54696 ( 9850) SS BOND : bond 0.00532 ( 1) SS BOND : angle 1.05824 ( 2) hydrogen bonds : bond 0.04346 ( 401) hydrogen bonds : angle 4.76305 ( 1161) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.300 Fit side-chains REVERT: A 17 LYS cc_start: 0.8377 (mttt) cc_final: 0.8007 (mttm) REVERT: A 32 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6370 (mtp85) REVERT: A 247 LEU cc_start: 0.7849 (mm) cc_final: 0.7565 (mm) REVERT: B 23 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7137 (tmmt) REVERT: B 96 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7711 (ttm110) REVERT: G 15 LEU cc_start: 0.7918 (tt) cc_final: 0.7715 (tp) REVERT: G 21 MET cc_start: 0.6408 (ttm) cc_final: 0.6182 (tmm) REVERT: R 187 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7167 (t) REVERT: R 326 TYR cc_start: 0.8120 (m-80) cc_final: 0.7744 (m-80) outliers start: 20 outliers final: 7 residues processed: 137 average time/residue: 0.5716 time to fit residues: 81.8601 Evaluate side-chains 117 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN R 109 ASN R 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133774 restraints weight = 8050.680| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.68 r_work: 0.3402 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7274 Z= 0.143 Angle : 0.528 7.356 9852 Z= 0.285 Chirality : 0.043 0.142 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.300 18.368 974 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.44 % Allowed : 15.03 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.28), residues: 889 helix: 1.88 (0.26), residues: 400 sheet: 0.28 (0.37), residues: 189 loop : -0.76 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.017 0.001 TYR B 105 PHE 0.010 0.001 PHE A 287 TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7272) covalent geometry : angle 0.52742 ( 9850) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.83564 ( 2) hydrogen bonds : bond 0.04289 ( 401) hydrogen bonds : angle 4.58612 ( 1161) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8398 (mttt) cc_final: 0.8042 (mttm) REVERT: A 28 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 29 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6866 (mttm) REVERT: A 32 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6509 (mtp85) REVERT: A 195 THR cc_start: 0.8037 (p) cc_final: 0.7733 (t) REVERT: A 247 LEU cc_start: 0.8154 (mm) cc_final: 0.7861 (mt) REVERT: B 23 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7165 (tmmt) REVERT: B 44 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7452 (mm-40) REVERT: B 96 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7710 (ttm110) REVERT: B 137 ARG cc_start: 0.8317 (mmt180) cc_final: 0.8065 (tpt170) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.6284 time to fit residues: 86.9946 Evaluate side-chains 125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 306 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132554 restraints weight = 8120.255| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.69 r_work: 0.3368 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7274 Z= 0.146 Angle : 0.529 7.533 9852 Z= 0.283 Chirality : 0.043 0.140 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.303 18.473 974 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.46 % Allowed : 16.18 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 889 helix: 1.86 (0.25), residues: 400 sheet: 0.29 (0.37), residues: 189 loop : -0.76 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.011 0.001 TYR B 105 PHE 0.010 0.001 PHE B 241 TRP 0.012 0.002 TRP R 226 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7272) covalent geometry : angle 0.52901 ( 9850) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.82279 ( 2) hydrogen bonds : bond 0.04216 ( 401) hydrogen bonds : angle 4.54447 ( 1161) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8401 (mttt) cc_final: 0.8030 (mttm) REVERT: A 28 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: A 29 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6919 (mttm) REVERT: A 32 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6778 (mtp85) REVERT: A 35 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8421 (mtpt) REVERT: A 195 THR cc_start: 0.8056 (p) cc_final: 0.7765 (t) REVERT: A 198 MET cc_start: 0.8313 (mtm) cc_final: 0.8086 (mtt) REVERT: A 247 LEU cc_start: 0.8170 (mm) cc_final: 0.7885 (mt) REVERT: A 305 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7576 (mmt-90) REVERT: B 23 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7168 (tmmt) REVERT: B 96 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7606 (ttm110) REVERT: B 137 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8126 (tpt170) REVERT: G 15 LEU cc_start: 0.8226 (tt) cc_final: 0.7814 (tp) REVERT: G 21 MET cc_start: 0.6256 (tmm) cc_final: 0.5972 (tmt) REVERT: R 100 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7069 (mmtm) REVERT: R 260 LYS cc_start: 0.7951 (mtpm) cc_final: 0.7650 (mtmp) outliers start: 35 outliers final: 17 residues processed: 132 average time/residue: 0.5871 time to fit residues: 81.5780 Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131794 restraints weight = 8145.801| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.72 r_work: 0.3356 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7274 Z= 0.145 Angle : 0.524 7.664 9852 Z= 0.281 Chirality : 0.043 0.139 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.303 18.361 974 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.71 % Allowed : 16.69 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 889 helix: 1.87 (0.25), residues: 400 sheet: 0.26 (0.37), residues: 187 loop : -0.82 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.013 0.001 TYR R 96 PHE 0.010 0.001 PHE B 241 TRP 0.014 0.002 TRP R 226 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7272) covalent geometry : angle 0.52389 ( 9850) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.77217 ( 2) hydrogen bonds : bond 0.04195 ( 401) hydrogen bonds : angle 4.52124 ( 1161) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.170 Fit side-chains REVERT: A 17 LYS cc_start: 0.8378 (mttt) cc_final: 0.8001 (mttm) REVERT: A 28 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: A 29 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6948 (mttm) REVERT: A 32 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6805 (mtp85) REVERT: A 35 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8389 (mtpt) REVERT: A 195 THR cc_start: 0.7982 (p) cc_final: 0.7741 (t) REVERT: A 247 LEU cc_start: 0.8216 (mm) cc_final: 0.7936 (mt) REVERT: A 294 ASN cc_start: 0.6662 (m110) cc_final: 0.6196 (t0) REVERT: B 23 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7178 (tmmt) REVERT: B 96 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7614 (ttm110) REVERT: B 137 ARG cc_start: 0.8305 (mmt180) cc_final: 0.8093 (tpt170) REVERT: G 21 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.6047 (tmt) outliers start: 37 outliers final: 18 residues processed: 135 average time/residue: 0.5567 time to fit residues: 78.8575 Evaluate side-chains 130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128468 restraints weight = 8219.724| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.74 r_work: 0.3301 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7274 Z= 0.236 Angle : 0.643 9.891 9852 Z= 0.340 Chirality : 0.047 0.167 1138 Planarity : 0.005 0.052 1234 Dihedral : 4.787 20.206 974 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.48 % Allowed : 17.58 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.28), residues: 889 helix: 1.67 (0.25), residues: 386 sheet: 0.12 (0.37), residues: 193 loop : -0.78 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.021 0.002 TYR R 96 PHE 0.015 0.002 PHE R 343 TRP 0.018 0.002 TRP R 226 HIS 0.005 0.002 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 7272) covalent geometry : angle 0.64278 ( 9850) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.03325 ( 2) hydrogen bonds : bond 0.04973 ( 401) hydrogen bonds : angle 4.81833 ( 1161) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.290 Fit side-chains REVERT: A 17 LYS cc_start: 0.8423 (mttt) cc_final: 0.8042 (mttm) REVERT: A 28 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: A 29 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7143 (mttm) REVERT: A 32 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6977 (mtp85) REVERT: A 35 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (mtpt) REVERT: A 294 ASN cc_start: 0.6788 (m110) cc_final: 0.6268 (t0) REVERT: B 23 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7339 (tmmt) REVERT: B 75 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: B 96 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7679 (ttm110) REVERT: B 137 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8054 (tpt170) REVERT: G 15 LEU cc_start: 0.8236 (tt) cc_final: 0.7870 (tp) REVERT: G 21 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.6010 (tmt) REVERT: R 71 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6148 (mp) REVERT: R 141 LYS cc_start: 0.6530 (mttp) cc_final: 0.6301 (mtpt) REVERT: R 260 LYS cc_start: 0.8308 (mtpm) cc_final: 0.7888 (mtpm) outliers start: 43 outliers final: 20 residues processed: 145 average time/residue: 0.5950 time to fit residues: 90.5619 Evaluate side-chains 133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132884 restraints weight = 8154.424| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.68 r_work: 0.3367 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7274 Z= 0.115 Angle : 0.516 9.033 9852 Z= 0.276 Chirality : 0.043 0.200 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.250 17.925 974 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.44 % Allowed : 20.76 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.28), residues: 889 helix: 1.89 (0.25), residues: 395 sheet: 0.21 (0.37), residues: 179 loop : -0.87 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.008 0.001 TYR R 149 PHE 0.008 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7272) covalent geometry : angle 0.51618 ( 9850) SS BOND : bond 0.00258 ( 1) SS BOND : angle 0.60145 ( 2) hydrogen bonds : bond 0.03934 ( 401) hydrogen bonds : angle 4.45495 ( 1161) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.257 Fit side-chains REVERT: A 17 LYS cc_start: 0.8365 (mttt) cc_final: 0.7990 (mttm) REVERT: A 29 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6950 (mttm) REVERT: A 32 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6890 (mpp80) REVERT: A 247 LEU cc_start: 0.8141 (mm) cc_final: 0.7840 (mm) REVERT: A 294 ASN cc_start: 0.6596 (m110) cc_final: 0.6081 (t0) REVERT: A 349 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7699 (mppt) REVERT: B 23 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7276 (tmmt) REVERT: B 96 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7641 (ttm110) REVERT: B 137 ARG cc_start: 0.8299 (mmt180) cc_final: 0.8041 (tpt170) REVERT: B 217 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7112 (pmt) REVERT: G 15 LEU cc_start: 0.8153 (tt) cc_final: 0.7762 (tp) REVERT: G 21 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5964 (tmt) REVERT: G 38 MET cc_start: 0.8213 (ptp) cc_final: 0.7842 (ptm) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 0.6260 time to fit residues: 84.8291 Evaluate side-chains 126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132703 restraints weight = 8190.065| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.71 r_work: 0.3362 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7274 Z= 0.123 Angle : 0.518 8.527 9852 Z= 0.276 Chirality : 0.043 0.177 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.178 18.196 974 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.20 % Allowed : 20.00 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.28), residues: 889 helix: 1.94 (0.25), residues: 396 sheet: 0.23 (0.37), residues: 188 loop : -0.90 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.017 0.001 TYR R 96 PHE 0.009 0.001 PHE B 241 TRP 0.013 0.002 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7272) covalent geometry : angle 0.51818 ( 9850) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.61769 ( 2) hydrogen bonds : bond 0.03928 ( 401) hydrogen bonds : angle 4.40416 ( 1161) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.307 Fit side-chains REVERT: A 17 LYS cc_start: 0.8373 (mttt) cc_final: 0.7998 (mttm) REVERT: A 29 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6945 (mttm) REVERT: A 32 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6980 (mpp80) REVERT: A 247 LEU cc_start: 0.8199 (mm) cc_final: 0.7884 (mm) REVERT: A 294 ASN cc_start: 0.6635 (m110) cc_final: 0.6116 (t0) REVERT: A 349 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7725 (mppt) REVERT: B 23 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7273 (tmmt) REVERT: B 44 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7423 (mm-40) REVERT: B 96 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7653 (ttm110) REVERT: B 137 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8043 (tpt170) REVERT: B 217 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7168 (pmt) REVERT: G 15 LEU cc_start: 0.8210 (tt) cc_final: 0.7822 (tp) REVERT: G 21 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5904 (tmt) REVERT: G 38 MET cc_start: 0.8219 (ptp) cc_final: 0.7868 (ptm) outliers start: 33 outliers final: 19 residues processed: 131 average time/residue: 0.5482 time to fit residues: 75.5518 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130414 restraints weight = 8151.952| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.72 r_work: 0.3356 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7274 Z= 0.130 Angle : 0.530 8.332 9852 Z= 0.282 Chirality : 0.043 0.170 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.185 18.265 974 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.82 % Allowed : 20.89 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 889 helix: 1.93 (0.25), residues: 397 sheet: 0.20 (0.37), residues: 189 loop : -0.86 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.007 0.001 TYR B 105 PHE 0.009 0.001 PHE B 241 TRP 0.019 0.002 TRP R 293 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7272) covalent geometry : angle 0.52983 ( 9850) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.58547 ( 2) hydrogen bonds : bond 0.03975 ( 401) hydrogen bonds : angle 4.39926 ( 1161) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.251 Fit side-chains REVERT: A 17 LYS cc_start: 0.8393 (mttt) cc_final: 0.8017 (mttm) REVERT: A 29 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6949 (mttm) REVERT: A 32 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6933 (mpp80) REVERT: A 247 LEU cc_start: 0.8259 (mm) cc_final: 0.7942 (mm) REVERT: A 294 ASN cc_start: 0.6647 (m110) cc_final: 0.6130 (t0) REVERT: A 349 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7715 (mppt) REVERT: B 23 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7279 (tmmt) REVERT: B 44 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7415 (mm-40) REVERT: B 96 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7678 (ttm110) REVERT: B 137 ARG cc_start: 0.8323 (mmt180) cc_final: 0.8069 (tpt170) REVERT: B 217 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7196 (pmt) REVERT: G 15 LEU cc_start: 0.8205 (tt) cc_final: 0.7821 (tp) REVERT: G 21 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5907 (tmt) REVERT: G 38 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7870 (ptm) outliers start: 30 outliers final: 18 residues processed: 124 average time/residue: 0.5146 time to fit residues: 67.0838 Evaluate side-chains 128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131828 restraints weight = 8140.820| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.68 r_work: 0.3365 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7274 Z= 0.125 Angle : 0.524 8.234 9852 Z= 0.279 Chirality : 0.043 0.166 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.148 18.161 974 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.31 % Allowed : 21.40 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.28), residues: 889 helix: 1.94 (0.25), residues: 397 sheet: 0.25 (0.37), residues: 187 loop : -0.84 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.015 0.001 TYR R 96 PHE 0.009 0.001 PHE B 241 TRP 0.022 0.002 TRP R 293 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7272) covalent geometry : angle 0.52425 ( 9850) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.64222 ( 2) hydrogen bonds : bond 0.03908 ( 401) hydrogen bonds : angle 4.38754 ( 1161) Misc. bond : bond 0.00015 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.316 Fit side-chains REVERT: A 17 LYS cc_start: 0.8369 (mttt) cc_final: 0.7995 (mttm) REVERT: A 29 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6943 (mttm) REVERT: A 32 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6982 (mpp80) REVERT: A 247 LEU cc_start: 0.8230 (mm) cc_final: 0.7913 (mm) REVERT: A 294 ASN cc_start: 0.6636 (m110) cc_final: 0.6109 (t0) REVERT: A 305 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7553 (mmt-90) REVERT: A 349 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7718 (mppt) REVERT: B 23 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7196 (tmmt) REVERT: B 96 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7645 (ttm110) REVERT: B 137 ARG cc_start: 0.8296 (mmt180) cc_final: 0.8038 (tpt170) REVERT: B 217 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7168 (pmt) REVERT: G 15 LEU cc_start: 0.8184 (tt) cc_final: 0.7800 (tp) REVERT: G 21 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5891 (tmt) REVERT: G 38 MET cc_start: 0.8224 (ptp) cc_final: 0.7873 (ptm) REVERT: R 190 CYS cc_start: 0.7768 (t) cc_final: 0.7558 (m) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.5706 time to fit residues: 75.6809 Evaluate side-chains 130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.168212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132585 restraints weight = 8122.225| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.69 r_work: 0.3366 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7274 Z= 0.118 Angle : 0.515 8.067 9852 Z= 0.274 Chirality : 0.043 0.174 1138 Planarity : 0.004 0.050 1234 Dihedral : 4.070 17.996 974 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.57 % Allowed : 20.89 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.28), residues: 889 helix: 2.00 (0.26), residues: 398 sheet: 0.24 (0.37), residues: 188 loop : -0.79 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.009 0.001 TYR R 149 PHE 0.009 0.001 PHE B 241 TRP 0.023 0.002 TRP R 293 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7272) covalent geometry : angle 0.51496 ( 9850) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.65406 ( 2) hydrogen bonds : bond 0.03806 ( 401) hydrogen bonds : angle 4.33331 ( 1161) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.48 seconds wall clock time: 50 minutes 42.61 seconds (3042.61 seconds total)