Starting phenix.real_space_refine on Sat Dec 28 18:54:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwl_37892/12_2024/8wwl_37892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwl_37892/12_2024/8wwl_37892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwl_37892/12_2024/8wwl_37892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwl_37892/12_2024/8wwl_37892.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwl_37892/12_2024/8wwl_37892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwl_37892/12_2024/8wwl_37892.cif" } resolution = 2.78 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= 0.001 sd= 0.070 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 68 5.16 5 C 5708 2.51 5 N 1518 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8964 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2239 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.61, per 1000 atoms: 0.63 Number of scatterers: 8964 At special positions: 0 Unit cell: (87.74, 119.84, 120.91, 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 68 16.00 O 1670 8.00 N 1518 7.00 C 5708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " 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=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 38.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.596A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.590A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.044A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.763A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.635A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.522A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 108 through 137 removed outlier: 3.638A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 removed outlier: 3.553A pdb=" N SER R 155 " --> pdb=" O ILE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 174 removed outlier: 3.605A pdb=" N MET R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 4.018A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.797A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.583A pdb=" N TYR R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.720A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.089A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix removed outlier: 3.542A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.345A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.562A 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: 5.734A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.609A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.941A 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: 6.140A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.720A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.647A 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: 6.941A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.402A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.880A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.257A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.209A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.537A pdb=" N VAL L 12 " --> pdb=" O LEU L 9 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2890 1.34 - 1.46: 2196 1.46 - 1.58: 3970 1.58 - 1.70: 0 1.70 - 1.81: 99 Bond restraints: 9155 Sorted by residual: bond pdb=" N VAL E 147 " pdb=" CA VAL E 147 " ideal model delta sigma weight residual 1.454 1.461 -0.006 7.70e-03 1.69e+04 6.88e-01 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.57e-01 bond pdb=" CA GLY A 292 " pdb=" C GLY A 292 " ideal model delta sigma weight residual 1.521 1.513 0.008 1.13e-02 7.83e+03 4.84e-01 bond pdb=" N GLY A 292 " pdb=" CA GLY A 292 " ideal model delta sigma weight residual 1.443 1.449 -0.006 8.60e-03 1.35e+04 4.12e-01 bond pdb=" C VAL E 64 " pdb=" O VAL E 64 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.30e-02 5.92e+03 3.91e-01 ... (remaining 9150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 12083 1.02 - 2.04: 281 2.04 - 3.06: 37 3.06 - 4.07: 13 4.07 - 5.09: 10 Bond angle restraints: 12424 Sorted by residual: angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 125.82 -3.08 1.44e+00 4.82e-01 4.59e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.25 -3.71 1.91e+00 2.74e-01 3.77e+00 angle pdb=" CA GLY A 292 " pdb=" C GLY A 292 " pdb=" N SER A 293 " ideal model delta sigma weight residual 114.30 116.61 -2.31 1.20e+00 6.94e-01 3.69e+00 angle pdb=" N GLY B 330 " pdb=" CA GLY B 330 " pdb=" C GLY B 330 " ideal model delta sigma weight residual 112.51 109.17 3.34 1.90e+00 2.77e-01 3.09e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 126.00 -2.53 1.53e+00 4.27e-01 2.74e+00 ... (remaining 12419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.06: 5148 14.06 - 28.12: 211 28.12 - 42.18: 47 42.18 - 56.24: 16 56.24 - 70.30: 4 Dihedral angle restraints: 5426 sinusoidal: 2060 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 5423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 857 0.026 - 0.052: 345 0.052 - 0.078: 126 0.078 - 0.105: 65 0.105 - 0.131: 32 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA VAL E 199 " pdb=" N VAL E 199 " pdb=" C VAL E 199 " pdb=" CB VAL E 199 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1422 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO B 236 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO E 107 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 194 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.016 5.00e-02 4.00e+02 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 188 2.69 - 3.24: 8567 3.24 - 3.79: 14268 3.79 - 4.35: 20357 4.35 - 4.90: 33380 Nonbonded interactions: 76760 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.197 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.274 3.040 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.275 3.120 nonbonded pdb=" O ALA R 364 " pdb=" OG SER R 367 " model vdw 2.278 3.040 ... (remaining 76755 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.002 0.032 9155 Z= 0.144 Angle : 0.415 5.092 12424 Z= 0.227 Chirality : 0.039 0.131 1425 Planarity : 0.003 0.049 1571 Dihedral : 8.895 70.304 3242 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.83 % Allowed : 3.41 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.49 (0.25), residues: 1144 helix: 0.53 (0.26), residues: 398 sheet: 0.54 (0.30), residues: 291 loop : 0.20 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE B 151 TYR 0.007 0.001 TYR E 103 ARG 0.002 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8280 (mttt) cc_final: 0.8033 (mtpt) REVERT: A 21 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7623 (mtm110) REVERT: A 25 GLU cc_start: 0.7724 (tt0) cc_final: 0.7457 (tm-30) REVERT: A 53 MET cc_start: 0.6223 (mtt) cc_final: 0.5954 (mtt) REVERT: A 186 GLU cc_start: 0.7970 (tt0) cc_final: 0.7752 (mt-10) REVERT: A 319 ILE cc_start: 0.8913 (mt) cc_final: 0.8704 (mm) REVERT: A 349 LYS cc_start: 0.8292 (mttt) cc_final: 0.7789 (mtmt) REVERT: B 96 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7318 (mtt-85) REVERT: B 130 GLU cc_start: 0.7946 (mp0) cc_final: 0.7599 (mt-10) REVERT: B 172 GLU cc_start: 0.7027 (tp30) cc_final: 0.6769 (tp30) REVERT: B 188 MET cc_start: 0.8779 (mmm) cc_final: 0.8261 (mmm) REVERT: B 189 SER cc_start: 0.8231 (p) cc_final: 0.7910 (t) REVERT: E 83 MET cc_start: 0.8883 (mtm) cc_final: 0.8427 (mtp) REVERT: E 85 SER cc_start: 0.8252 (m) cc_final: 0.7889 (t) REVERT: E 90 ASP cc_start: 0.8183 (m-30) cc_final: 0.7978 (m-30) REVERT: R 165 MET cc_start: 0.8508 (ttm) cc_final: 0.8292 (tmm) REVERT: R 191 MET cc_start: 0.7686 (tpt) cc_final: 0.7238 (ttt) REVERT: R 225 LYS cc_start: 0.8284 (mttt) cc_final: 0.8072 (mppt) outliers start: 8 outliers final: 4 residues processed: 191 average time/residue: 1.3898 time to fit residues: 281.9582 Evaluate side-chains 146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 155 ASN B 220 GLN B 259 GLN E 183 GLN R 194 ASN R 281 GLN R 376 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9155 Z= 0.231 Angle : 0.535 6.427 12424 Z= 0.292 Chirality : 0.043 0.137 1425 Planarity : 0.004 0.049 1571 Dihedral : 5.137 55.310 1259 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 9.40 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.02 (0.25), residues: 1144 helix: 1.71 (0.26), residues: 395 sheet: 0.32 (0.30), residues: 287 loop : 0.13 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 179 PHE 0.016 0.002 PHE A 196 TYR 0.012 0.001 TYR R 341 ARG 0.007 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8182 (mttt) cc_final: 0.7951 (mtpt) REVERT: A 21 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7485 (mtm110) REVERT: A 25 GLU cc_start: 0.7557 (tt0) cc_final: 0.7152 (tt0) REVERT: A 53 MET cc_start: 0.6187 (mtt) cc_final: 0.5879 (mtt) REVERT: A 186 GLU cc_start: 0.7831 (tt0) cc_final: 0.7566 (mt-10) REVERT: A 349 LYS cc_start: 0.7965 (mttt) cc_final: 0.7493 (mtpt) REVERT: B 96 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7454 (mtt-85) REVERT: B 130 GLU cc_start: 0.7990 (mp0) cc_final: 0.7659 (mt-10) REVERT: B 146 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 188 MET cc_start: 0.8776 (mmm) cc_final: 0.8319 (mmm) REVERT: B 189 SER cc_start: 0.8279 (p) cc_final: 0.7872 (t) REVERT: B 217 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6959 (pp-130) REVERT: B 219 ARG cc_start: 0.7161 (mmm160) cc_final: 0.6685 (mmt180) REVERT: C 21 MET cc_start: 0.7645 (mmm) cc_final: 0.7119 (ttp) REVERT: E 83 MET cc_start: 0.8837 (mtm) cc_final: 0.8396 (mtp) REVERT: E 179 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: R 169 ILE cc_start: 0.7515 (pt) cc_final: 0.6934 (mm) REVERT: R 191 MET cc_start: 0.7477 (tpt) cc_final: 0.6985 (ttt) REVERT: R 235 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8060 (mt) REVERT: R 315 SER cc_start: 0.6773 (m) cc_final: 0.6366 (p) outliers start: 25 outliers final: 11 residues processed: 156 average time/residue: 1.3897 time to fit residues: 230.2065 Evaluate side-chains 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9155 Z= 0.191 Angle : 0.492 6.244 12424 Z= 0.266 Chirality : 0.041 0.136 1425 Planarity : 0.004 0.050 1571 Dihedral : 4.666 57.842 1257 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.79 % Allowed : 10.12 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.20 (0.25), residues: 1144 helix: 2.14 (0.26), residues: 394 sheet: 0.24 (0.30), residues: 293 loop : 0.09 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE A 196 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8103 (mttt) cc_final: 0.7885 (mtmt) REVERT: A 21 ARG cc_start: 0.7764 (ttm170) cc_final: 0.7415 (mtm110) REVERT: A 25 GLU cc_start: 0.7484 (tt0) cc_final: 0.7064 (tm-30) REVERT: A 53 MET cc_start: 0.6017 (mtt) cc_final: 0.5769 (mtt) REVERT: A 186 GLU cc_start: 0.7801 (tt0) cc_final: 0.7555 (mt-10) REVERT: A 330 LYS cc_start: 0.7122 (mtmm) cc_final: 0.5982 (tttp) REVERT: A 349 LYS cc_start: 0.7927 (mttt) cc_final: 0.7478 (mtpt) REVERT: B 96 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7469 (mtt-85) REVERT: B 130 GLU cc_start: 0.7969 (mp0) cc_final: 0.7677 (mt-10) REVERT: B 188 MET cc_start: 0.8760 (mmm) cc_final: 0.8323 (mmm) REVERT: B 189 SER cc_start: 0.8240 (p) cc_final: 0.7849 (t) REVERT: B 217 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6881 (pp-130) REVERT: B 219 ARG cc_start: 0.7062 (mmm160) cc_final: 0.6658 (mmt180) REVERT: B 274 THR cc_start: 0.8617 (p) cc_final: 0.8376 (p) REVERT: C 21 MET cc_start: 0.7607 (mmm) cc_final: 0.7102 (ttp) REVERT: E 83 MET cc_start: 0.8804 (mtm) cc_final: 0.8384 (mtp) REVERT: E 93 MET cc_start: 0.8610 (ttt) cc_final: 0.8144 (tpp) REVERT: E 179 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: R 139 LYS cc_start: 0.8106 (mttt) cc_final: 0.7808 (mtpt) REVERT: R 184 MET cc_start: 0.6932 (mmm) cc_final: 0.6604 (tpt) REVERT: R 191 MET cc_start: 0.7434 (tpt) cc_final: 0.6947 (ttt) REVERT: R 235 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8165 (mt) REVERT: R 315 SER cc_start: 0.6698 (m) cc_final: 0.6279 (p) outliers start: 27 outliers final: 14 residues processed: 162 average time/residue: 1.4325 time to fit residues: 245.8429 Evaluate side-chains 157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.0070 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 176 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9155 Z= 0.177 Angle : 0.478 6.431 12424 Z= 0.256 Chirality : 0.041 0.135 1425 Planarity : 0.004 0.050 1571 Dihedral : 4.627 58.964 1257 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.31 % Allowed : 10.33 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.25 (0.25), residues: 1144 helix: 2.28 (0.26), residues: 396 sheet: 0.20 (0.30), residues: 284 loop : 0.05 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE A 196 TYR 0.011 0.001 TYR R 341 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.040 Fit side-chains REVERT: A 21 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7473 (mtm110) REVERT: A 25 GLU cc_start: 0.7534 (tt0) cc_final: 0.7114 (tm-30) REVERT: A 186 GLU cc_start: 0.7788 (tt0) cc_final: 0.7550 (mt-10) REVERT: A 209 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7657 (pptt) REVERT: A 330 LYS cc_start: 0.7139 (mtmm) cc_final: 0.5951 (tttp) REVERT: A 349 LYS cc_start: 0.7872 (mttt) cc_final: 0.7438 (ttmt) REVERT: B 96 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7434 (mtt-85) REVERT: B 130 GLU cc_start: 0.7953 (mp0) cc_final: 0.7684 (mt-10) REVERT: B 188 MET cc_start: 0.8754 (mmm) cc_final: 0.8363 (mmm) REVERT: B 189 SER cc_start: 0.8221 (p) cc_final: 0.7820 (t) REVERT: B 217 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6898 (pp-130) REVERT: B 219 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6644 (mmt180) REVERT: B 274 THR cc_start: 0.8562 (p) cc_final: 0.8300 (p) REVERT: C 21 MET cc_start: 0.7588 (mmm) cc_final: 0.7071 (ttp) REVERT: E 83 MET cc_start: 0.8777 (mtm) cc_final: 0.8400 (mtp) REVERT: E 93 MET cc_start: 0.8599 (ttt) cc_final: 0.8103 (tpp) REVERT: E 179 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: R 191 MET cc_start: 0.7256 (tpt) cc_final: 0.6777 (ttt) REVERT: R 235 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8177 (mt) REVERT: R 315 SER cc_start: 0.6637 (m) cc_final: 0.6246 (p) REVERT: R 332 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7924 (tp) outliers start: 32 outliers final: 16 residues processed: 155 average time/residue: 1.3920 time to fit residues: 228.9482 Evaluate side-chains 156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9155 Z= 0.220 Angle : 0.498 6.608 12424 Z= 0.266 Chirality : 0.042 0.135 1425 Planarity : 0.004 0.050 1571 Dihedral : 4.728 57.911 1257 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.31 % Allowed : 10.54 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.16 (0.25), residues: 1144 helix: 2.25 (0.26), residues: 400 sheet: 0.16 (0.30), residues: 285 loop : -0.08 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 196 TYR 0.010 0.001 TYR E 103 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.991 Fit side-chains REVERT: A 21 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7472 (mtm110) REVERT: A 25 GLU cc_start: 0.7496 (tt0) cc_final: 0.7059 (tm-30) REVERT: A 186 GLU cc_start: 0.7796 (tt0) cc_final: 0.7545 (mt-10) REVERT: A 330 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6013 (tttp) REVERT: A 349 LYS cc_start: 0.7866 (mttt) cc_final: 0.7407 (ttmt) REVERT: B 96 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7431 (mtt-85) REVERT: B 130 GLU cc_start: 0.7991 (mp0) cc_final: 0.7699 (tt0) REVERT: B 146 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 188 MET cc_start: 0.8745 (mmm) cc_final: 0.8386 (mmm) REVERT: B 189 SER cc_start: 0.8232 (p) cc_final: 0.7836 (t) REVERT: B 217 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6984 (pp-130) REVERT: B 219 ARG cc_start: 0.7083 (mmm160) cc_final: 0.6623 (mmt180) REVERT: C 21 MET cc_start: 0.7668 (mmm) cc_final: 0.7146 (ttp) REVERT: E 83 MET cc_start: 0.8811 (mtm) cc_final: 0.8310 (mtp) REVERT: E 93 MET cc_start: 0.8597 (ttt) cc_final: 0.8092 (tpp) REVERT: E 179 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: R 184 MET cc_start: 0.7105 (mmm) cc_final: 0.6825 (tpt) REVERT: R 191 MET cc_start: 0.7254 (tpt) cc_final: 0.6765 (ttt) REVERT: R 235 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8189 (mt) outliers start: 32 outliers final: 19 residues processed: 149 average time/residue: 1.3873 time to fit residues: 219.2394 Evaluate side-chains 151 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9155 Z= 0.181 Angle : 0.478 6.823 12424 Z= 0.255 Chirality : 0.041 0.142 1425 Planarity : 0.004 0.050 1571 Dihedral : 4.666 59.930 1257 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.00 % Allowed : 11.05 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.23 (0.25), residues: 1144 helix: 2.40 (0.26), residues: 398 sheet: 0.18 (0.30), residues: 285 loop : -0.11 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE A 196 TYR 0.011 0.001 TYR E 190 ARG 0.009 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.105 Fit side-chains REVERT: A 21 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7501 (mtm110) REVERT: A 25 GLU cc_start: 0.7491 (tt0) cc_final: 0.7079 (tt0) REVERT: A 330 LYS cc_start: 0.7250 (mtmm) cc_final: 0.6029 (tttp) REVERT: A 349 LYS cc_start: 0.7816 (mttt) cc_final: 0.7391 (ttmt) REVERT: B 96 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7445 (mtt-85) REVERT: B 130 GLU cc_start: 0.7973 (mp0) cc_final: 0.7696 (tt0) REVERT: B 188 MET cc_start: 0.8727 (mmm) cc_final: 0.8369 (mmm) REVERT: B 189 SER cc_start: 0.8193 (p) cc_final: 0.7789 (t) REVERT: B 217 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6973 (pp-130) REVERT: B 219 ARG cc_start: 0.7026 (mmm160) cc_final: 0.6580 (mmt180) REVERT: C 21 MET cc_start: 0.7672 (mmm) cc_final: 0.7080 (ttp) REVERT: E 83 MET cc_start: 0.8801 (mtm) cc_final: 0.8348 (mtp) REVERT: E 93 MET cc_start: 0.8601 (ttt) cc_final: 0.8097 (tpp) REVERT: E 179 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: R 139 LYS cc_start: 0.8072 (mttt) cc_final: 0.7868 (mtpt) REVERT: R 184 MET cc_start: 0.7067 (mmm) cc_final: 0.6725 (tpt) REVERT: R 191 MET cc_start: 0.7242 (tpt) cc_final: 0.6773 (ttt) REVERT: R 235 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8202 (mt) outliers start: 29 outliers final: 19 residues processed: 143 average time/residue: 1.4720 time to fit residues: 223.0697 Evaluate side-chains 149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9155 Z= 0.219 Angle : 0.508 8.623 12424 Z= 0.267 Chirality : 0.042 0.141 1425 Planarity : 0.004 0.050 1571 Dihedral : 4.747 59.926 1257 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.41 % Allowed : 11.16 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.23 (0.25), residues: 1144 helix: 2.36 (0.26), residues: 400 sheet: 0.18 (0.30), residues: 290 loop : -0.08 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 196 TYR 0.010 0.001 TYR E 103 ARG 0.010 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.999 Fit side-chains REVERT: A 21 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7486 (mtm110) REVERT: A 25 GLU cc_start: 0.7508 (tt0) cc_final: 0.7111 (tt0) REVERT: A 330 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6039 (tttp) REVERT: A 349 LYS cc_start: 0.7821 (mttt) cc_final: 0.7411 (ttmt) REVERT: B 96 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7434 (mtt-85) REVERT: B 130 GLU cc_start: 0.7964 (mp0) cc_final: 0.7685 (tt0) REVERT: B 146 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 188 MET cc_start: 0.8743 (mmm) cc_final: 0.8252 (mmm) REVERT: B 189 SER cc_start: 0.8228 (p) cc_final: 0.7837 (t) REVERT: B 217 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.6752 (pp-130) REVERT: B 219 ARG cc_start: 0.7062 (mmm160) cc_final: 0.6466 (mmm160) REVERT: C 21 MET cc_start: 0.7673 (mmm) cc_final: 0.7106 (ttp) REVERT: E 38 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8166 (ptt180) REVERT: E 83 MET cc_start: 0.8788 (mtm) cc_final: 0.8343 (mtp) REVERT: E 93 MET cc_start: 0.8618 (ttt) cc_final: 0.8119 (tpp) REVERT: E 179 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: R 184 MET cc_start: 0.7076 (mmm) cc_final: 0.6725 (tpt) REVERT: R 191 MET cc_start: 0.7210 (tpt) cc_final: 0.6765 (ttt) REVERT: R 235 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8208 (mt) REVERT: R 266 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7570 (mtt-85) REVERT: R 325 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6498 (ttp80) outliers start: 33 outliers final: 20 residues processed: 141 average time/residue: 1.4055 time to fit residues: 210.1857 Evaluate side-chains 150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 53 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 chunk 95 optimal weight: 0.0870 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.002 0.030 9155 Z= 0.124 Angle : 0.451 7.604 12424 Z= 0.240 Chirality : 0.040 0.141 1425 Planarity : 0.003 0.050 1571 Dihedral : 4.366 52.902 1257 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.38 % Allowed : 12.19 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.42 (0.25), residues: 1144 helix: 2.62 (0.26), residues: 395 sheet: 0.28 (0.30), residues: 288 loop : -0.05 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.009 0.001 PHE A 189 TYR 0.013 0.001 TYR E 190 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.031 Fit side-chains REVERT: A 25 GLU cc_start: 0.7514 (tt0) cc_final: 0.7106 (tt0) REVERT: A 330 LYS cc_start: 0.7206 (mtmm) cc_final: 0.6027 (tttp) REVERT: A 349 LYS cc_start: 0.7793 (mttt) cc_final: 0.7434 (ttmt) REVERT: B 96 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7397 (mtt-85) REVERT: B 130 GLU cc_start: 0.7898 (mp0) cc_final: 0.7657 (tt0) REVERT: B 188 MET cc_start: 0.8712 (mmm) cc_final: 0.8336 (mmm) REVERT: B 189 SER cc_start: 0.8146 (p) cc_final: 0.7722 (t) REVERT: C 21 MET cc_start: 0.7728 (mmm) cc_final: 0.7308 (ttp) REVERT: E 11 LEU cc_start: 0.8595 (tp) cc_final: 0.8358 (tt) REVERT: E 83 MET cc_start: 0.8725 (mtm) cc_final: 0.8286 (mtp) REVERT: E 93 MET cc_start: 0.8582 (ttt) cc_final: 0.8096 (tpp) REVERT: R 184 MET cc_start: 0.6920 (mmm) cc_final: 0.6606 (tpt) REVERT: R 191 MET cc_start: 0.7116 (tpt) cc_final: 0.6736 (ttt) REVERT: R 266 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7465 (mtt-85) outliers start: 23 outliers final: 12 residues processed: 145 average time/residue: 1.3960 time to fit residues: 214.6285 Evaluate side-chains 131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9155 Z= 0.199 Angle : 0.500 7.495 12424 Z= 0.264 Chirality : 0.042 0.153 1425 Planarity : 0.004 0.049 1571 Dihedral : 4.553 55.153 1257 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.17 % Allowed : 13.33 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.38 (0.25), residues: 1144 helix: 2.53 (0.26), residues: 398 sheet: 0.32 (0.30), residues: 284 loop : -0.08 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 196 TYR 0.012 0.001 TYR R 341 ARG 0.008 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.049 Fit side-chains REVERT: A 25 GLU cc_start: 0.7532 (tt0) cc_final: 0.7127 (tt0) REVERT: A 330 LYS cc_start: 0.7223 (mtmm) cc_final: 0.6041 (tttp) REVERT: A 349 LYS cc_start: 0.7805 (mttt) cc_final: 0.7413 (ttmt) REVERT: B 96 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7449 (mtt-85) REVERT: B 130 GLU cc_start: 0.7941 (mp0) cc_final: 0.7689 (tt0) REVERT: B 146 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 188 MET cc_start: 0.8737 (mmm) cc_final: 0.8374 (mmm) REVERT: B 189 SER cc_start: 0.8189 (p) cc_final: 0.7778 (t) REVERT: C 21 MET cc_start: 0.7707 (mmm) cc_final: 0.7087 (ttm) REVERT: E 11 LEU cc_start: 0.8602 (tp) cc_final: 0.8345 (tt) REVERT: E 83 MET cc_start: 0.8775 (mtm) cc_final: 0.8300 (mtp) REVERT: R 184 MET cc_start: 0.7000 (mmm) cc_final: 0.6699 (tpt) REVERT: R 191 MET cc_start: 0.7422 (tpt) cc_final: 0.6877 (ttt) REVERT: R 266 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7562 (mtt-85) REVERT: R 345 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8158 (tp40) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 1.3848 time to fit residues: 198.5481 Evaluate side-chains 136 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9155 Z= 0.219 Angle : 0.516 7.523 12424 Z= 0.271 Chirality : 0.042 0.158 1425 Planarity : 0.004 0.049 1571 Dihedral : 4.661 56.536 1257 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.17 % Allowed : 13.33 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.34 (0.25), residues: 1144 helix: 2.49 (0.26), residues: 398 sheet: 0.32 (0.30), residues: 285 loop : -0.10 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 248 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE A 196 TYR 0.010 0.001 TYR R 342 ARG 0.009 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.092 Fit side-chains REVERT: A 25 GLU cc_start: 0.7530 (tt0) cc_final: 0.7096 (tm-30) REVERT: A 312 LYS cc_start: 0.7691 (tppt) cc_final: 0.7384 (mmpt) REVERT: A 330 LYS cc_start: 0.7238 (mtmm) cc_final: 0.6049 (tttp) REVERT: A 349 LYS cc_start: 0.7809 (mttt) cc_final: 0.7416 (ttmt) REVERT: B 96 ARG cc_start: 0.7832 (mtt180) cc_final: 0.7454 (mtt-85) REVERT: B 130 GLU cc_start: 0.7954 (mp0) cc_final: 0.7694 (tt0) REVERT: B 146 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (mp) REVERT: B 188 MET cc_start: 0.8738 (mmm) cc_final: 0.8246 (mmm) REVERT: B 189 SER cc_start: 0.8224 (p) cc_final: 0.7823 (t) REVERT: C 21 MET cc_start: 0.7714 (mmm) cc_final: 0.7154 (ttp) REVERT: E 11 LEU cc_start: 0.8602 (tp) cc_final: 0.8348 (tt) REVERT: E 83 MET cc_start: 0.8795 (mtm) cc_final: 0.8321 (mtp) REVERT: E 93 MET cc_start: 0.8605 (ttt) cc_final: 0.8186 (tpp) REVERT: R 184 MET cc_start: 0.7117 (mmm) cc_final: 0.6764 (tpt) REVERT: R 191 MET cc_start: 0.7425 (tpt) cc_final: 0.6875 (ttt) REVERT: R 266 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7487 (mtt-85) REVERT: R 345 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8126 (tp40) outliers start: 21 outliers final: 17 residues processed: 134 average time/residue: 1.5230 time to fit residues: 216.0020 Evaluate side-chains 136 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.171337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135159 restraints weight = 9389.403| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.66 r_work: 0.3314 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9155 Z= 0.206 Angle : 0.512 7.553 12424 Z= 0.269 Chirality : 0.042 0.141 1425 Planarity : 0.004 0.048 1571 Dihedral : 4.664 56.030 1257 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.17 % Allowed : 13.53 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.32 (0.25), residues: 1144 helix: 2.48 (0.26), residues: 398 sheet: 0.26 (0.30), residues: 287 loop : -0.09 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 248 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE A 196 TYR 0.010 0.001 TYR R 342 ARG 0.009 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.75 seconds wall clock time: 72 minutes 17.48 seconds (4337.48 seconds total)