Starting phenix.real_space_refine on Thu Jul 2 11:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.map" model { file = "/net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xow_33361/07_2026/7xow_33361.cif" } resolution = 3.1 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= 0.007 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 5479 2.51 5 N 1468 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8566 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2153 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1798 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 75 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.04, per 1000 atoms: 0.24 Number of scatterers: 8566 At special positions: 0 Unit cell: (112.554, 115.596, 124.722, 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 1561 8.00 N 1468 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 571.6 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 36.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 54 through 81 Processing helix chain 'R' and resid 87 through 108 removed outlier: 4.032A pdb=" N ALA R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 118 Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 122 through 158 removed outlier: 4.142A pdb=" N ILE R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 166 removed outlier: 4.291A pdb=" N VAL R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 186 removed outlier: 3.711A pdb=" N ARG R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 214 through 228 Processing helix chain 'R' and resid 228 through 248 removed outlier: 3.832A pdb=" N GLY R 248 " --> pdb=" O GLU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 360 removed outlier: 4.413A pdb=" N VAL R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 360 through 367 removed outlier: 3.876A pdb=" N HIS R 364 " --> pdb=" O GLY R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 391 removed outlier: 3.569A pdb=" N PHE R 374 " --> pdb=" O ALA R 370 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER R 382 " --> pdb=" O LEU R 378 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 396 through 403 removed outlier: 3.787A pdb=" N ALA R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.856A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.911A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.738A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.826A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.627A pdb=" N THR A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.036A pdb=" N TYR A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.710A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.813A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.888A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.704A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.534A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.737A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.916A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.557A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB3, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.689A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 183 through 189 removed outlier: 7.147A pdb=" N LEU A 34 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 198 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 200 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 38 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 183 through 189 removed outlier: 7.147A pdb=" N LEU A 34 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 198 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 200 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 38 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1188 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: 1.38 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1467 1.32 - 1.45: 2344 1.45 - 1.57: 4849 1.57 - 1.69: 1 1.69 - 1.82: 85 Bond restraints: 8746 Sorted by residual: bond pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" OH TYS L 12 " pdb=" S TYS L 12 " ideal model delta sigma weight residual 1.679 1.538 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C TYR R 189 " pdb=" O TYR R 189 " ideal model delta sigma weight residual 1.244 1.202 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" N LEU R 203 " pdb=" CA LEU R 203 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 1.458 1.482 -0.025 1.41e-02 5.03e+03 3.06e+00 ... (remaining 8741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.93: 11867 5.93 - 11.86: 10 11.86 - 17.79: 2 17.79 - 23.72: 1 23.72 - 29.64: 2 Bond angle restraints: 11882 Sorted by residual: angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O2 TYS L 12 " ideal model delta sigma weight residual 114.11 84.47 29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" O1 TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 115.16 88.07 27.09 3.00e+00 1.11e-01 8.16e+01 angle pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" C VAL R 202 " ideal model delta sigma weight residual 110.62 118.97 -8.35 1.02e+00 9.61e-01 6.71e+01 angle pdb=" N GLN R 204 " pdb=" CA GLN R 204 " pdb=" C GLN R 204 " ideal model delta sigma weight residual 111.17 121.67 -10.50 1.41e+00 5.03e-01 5.54e+01 angle pdb=" OH TYS L 12 " pdb=" S TYS L 12 " pdb=" O3 TYS L 12 " ideal model delta sigma weight residual 100.21 118.72 -18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 11877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4694 17.60 - 35.19: 391 35.19 - 52.79: 60 52.79 - 70.39: 10 70.39 - 87.98: 4 Dihedral angle restraints: 5159 sinusoidal: 1913 harmonic: 3246 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 dihedral pdb=" C VAL R 202 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " pdb=" CB VAL R 202 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA LEU A 265 " pdb=" C LEU A 265 " pdb=" N PHE A 266 " pdb=" CA PHE A 266 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1186 0.067 - 0.134: 168 0.134 - 0.201: 10 0.201 - 0.269: 6 0.269 - 0.336: 4 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE L 17 " pdb=" N PHE L 17 " pdb=" C PHE L 17 " pdb=" CB PHE L 17 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA GLN R 204 " pdb=" N GLN R 204 " pdb=" C GLN R 204 " pdb=" CB GLN R 204 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA VAL R 202 " pdb=" N VAL R 202 " pdb=" C VAL R 202 " pdb=" CB VAL R 202 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1371 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 189 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO R 190 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO E 224 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 187 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO R 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 188 " -0.047 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 738 2.74 - 3.28: 8406 3.28 - 3.82: 13468 3.82 - 4.36: 16062 4.36 - 4.90: 29053 Nonbonded interactions: 67727 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 228 " pdb=" NZ LYS A 209 " model vdw 2.244 3.120 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.268 3.120 nonbonded pdb=" N CYS A 324 " pdb=" OD2 ASP A 327 " model vdw 2.269 3.120 ... (remaining 67722 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: 0.410 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.005 0.170 8748 Z= 0.233 Angle : 0.857 29.645 11886 Z= 0.455 Chirality : 0.052 0.336 1374 Planarity : 0.006 0.105 1495 Dihedral : 13.161 87.985 3059 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -2.76 (0.23), residues: 1097 helix: -0.41 (0.26), residues: 364 sheet: -1.79 (0.29), residues: 289 loop : -3.05 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 57 TYR 0.013 0.001 TYR R 192 PHE 0.022 0.002 PHE B 234 TRP 0.027 0.002 TRP E 111 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 ( 8746) covalent geometry : angle 0.85659 / 0.45 (11882) SS BOND : bond 0.00517 / 0.25 ( 2) SS BOND : angle 1.56428 / 0.81 ( 4) hydrogen bonds : bond 0.14300 / 9.33 ( 410) hydrogen bonds : angle 6.50579 / 4.83 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.330 Fit side-chains REVERT: R 73 MET cc_start: 0.7231 (mmt) cc_final: 0.6878 (mmt) REVERT: R 207 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.5572 (m-70) REVERT: R 213 ARG cc_start: 0.6193 (mmt180) cc_final: 0.3788 (ptt-90) REVERT: R 333 ARG cc_start: 0.6314 (ttm170) cc_final: 0.5644 (ttm-80) REVERT: R 398 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6744 (mmp80) REVERT: B 67 SER cc_start: 0.8803 (m) cc_final: 0.8404 (t) REVERT: B 325 MET cc_start: 0.7886 (tpp) cc_final: 0.7674 (tpp) REVERT: E 182 ASN cc_start: 0.8736 (m110) cc_final: 0.8462 (m110) REVERT: A 242 MET cc_start: 0.7403 (tpp) cc_final: 0.6316 (tpp) REVERT: A 305 LYS cc_start: 0.7059 (ttpp) cc_final: 0.6810 (tppt) REVERT: A 339 LYS cc_start: 0.7160 (tttt) cc_final: 0.6952 (tttp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1124 time to fit residues: 25.1939 Evaluate side-chains 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 chunk 106 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 166 GLN R 196 GLN R 204 GLN B 17 GLN B 35 ASN B 176 GLN B 220 GLN C 44 HIS E 159 ASN E 167 GLN E 171 GLN A 231 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.187638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149093 restraints weight = 9149.646| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.91 r_work: 0.3654 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8748 Z= 0.115 Angle : 0.589 8.417 11886 Z= 0.300 Chirality : 0.043 0.153 1374 Planarity : 0.005 0.081 1495 Dihedral : 4.701 38.728 1219 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 1.79 % Allowed : 10.08 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.49 (0.25), residues: 1097 helix: 0.97 (0.28), residues: 366 sheet: -1.29 (0.30), residues: 285 loop : -2.48 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 179 TYR 0.023 0.001 TYR R 380 PHE 0.015 0.001 PHE A 49 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8746) covalent geometry : angle 0.58710 / 0.30 (11882) SS BOND : bond 0.00768 / 0.40 ( 2) SS BOND : angle 2.38010 / 1.32 ( 4) hydrogen bonds : bond 0.03678 / 2.56 ( 410) hydrogen bonds : angle 4.90258 / 3.56 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.329 Fit side-chains REVERT: R 207 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.5174 (m-70) REVERT: R 213 ARG cc_start: 0.6068 (mmt180) cc_final: 0.3489 (ptt-90) REVERT: R 333 ARG cc_start: 0.6648 (ttm170) cc_final: 0.5671 (ttm-80) REVERT: R 380 TYR cc_start: 0.7327 (m-80) cc_final: 0.6948 (m-80) REVERT: R 398 ARG cc_start: 0.6800 (mmt90) cc_final: 0.6407 (mmp80) REVERT: B 258 ASP cc_start: 0.8442 (t0) cc_final: 0.7549 (t0) REVERT: B 325 MET cc_start: 0.8220 (tpp) cc_final: 0.7789 (tpp) REVERT: E 180 MET cc_start: 0.7996 (ptm) cc_final: 0.7792 (ptm) REVERT: A 242 MET cc_start: 0.7328 (tpp) cc_final: 0.6275 (tpp) REVERT: A 305 LYS cc_start: 0.6712 (ttpp) cc_final: 0.6441 (tppt) REVERT: A 339 LYS cc_start: 0.7140 (tttt) cc_final: 0.6935 (tttp) outliers start: 16 outliers final: 8 residues processed: 158 average time/residue: 0.0946 time to fit residues: 20.8121 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 196 GLN B 220 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145473 restraints weight = 9163.023| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.81 r_work: 0.3425 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8748 Z= 0.130 Angle : 0.596 8.513 11886 Z= 0.302 Chirality : 0.043 0.177 1374 Planarity : 0.004 0.081 1495 Dihedral : 4.662 38.384 1219 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 2.91 % Allowed : 12.21 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.01 (0.26), residues: 1097 helix: 1.38 (0.28), residues: 367 sheet: -1.02 (0.30), residues: 285 loop : -2.21 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.018 0.001 TYR A 285 PHE 0.014 0.001 PHE A 49 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8746) covalent geometry : angle 0.59410 / 0.30 (11882) SS BOND : bond 0.00789 / 0.40 ( 2) SS BOND : angle 2.53356 / 1.42 ( 4) hydrogen bonds : bond 0.03558 / 2.48 ( 410) hydrogen bonds : angle 4.59682 / 3.32 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.326 Fit side-chains REVERT: R 184 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6823 (mp) REVERT: R 196 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.5673 (mp10) REVERT: R 213 ARG cc_start: 0.6020 (mmt180) cc_final: 0.3327 (ptt-90) REVERT: R 244 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5092 (mp0) REVERT: R 333 ARG cc_start: 0.6552 (ttm170) cc_final: 0.5478 (ttm-80) REVERT: R 380 TYR cc_start: 0.6947 (m-80) cc_final: 0.6546 (m-80) REVERT: R 398 ARG cc_start: 0.6523 (mmt90) cc_final: 0.6192 (mmp80) REVERT: B 137 ARG cc_start: 0.7986 (mmm160) cc_final: 0.6986 (tpp-160) REVERT: B 258 ASP cc_start: 0.8227 (t0) cc_final: 0.7464 (t0) REVERT: B 262 MET cc_start: 0.7586 (ttm) cc_final: 0.7385 (ttm) REVERT: B 325 MET cc_start: 0.7953 (tpp) cc_final: 0.7443 (tpp) REVERT: E 30 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (t) REVERT: E 82 GLN cc_start: 0.7001 (tp40) cc_final: 0.6684 (tp40) REVERT: E 126 ILE cc_start: 0.7778 (mp) cc_final: 0.7470 (mt) REVERT: E 146 SER cc_start: 0.8459 (t) cc_final: 0.8120 (p) REVERT: A 196 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7754 (ttm-80) REVERT: A 305 LYS cc_start: 0.6401 (ttpp) cc_final: 0.6196 (tppt) REVERT: A 327 ASP cc_start: 0.5152 (OUTLIER) cc_final: 0.4903 (m-30) REVERT: L 15 MET cc_start: 0.6863 (ptp) cc_final: 0.6329 (mtp) outliers start: 26 outliers final: 15 residues processed: 150 average time/residue: 0.0948 time to fit residues: 19.9699 Evaluate side-chains 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 204 GLN B 220 GLN A 321 HIS A 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.186650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148349 restraints weight = 9155.991| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.89 r_work: 0.3623 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8748 Z= 0.148 Angle : 0.602 7.691 11886 Z= 0.305 Chirality : 0.044 0.189 1374 Planarity : 0.004 0.082 1495 Dihedral : 4.621 39.287 1217 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.80 % Allowed : 14.00 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.84 (0.26), residues: 1097 helix: 1.52 (0.28), residues: 366 sheet: -0.97 (0.30), residues: 287 loop : -2.07 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.011 0.001 TYR A 285 PHE 0.015 0.001 PHE E 27 TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8746) covalent geometry : angle 0.59990 / 0.30 (11882) SS BOND : bond 0.00853 / 0.44 ( 2) SS BOND : angle 2.68259 / 1.49 ( 4) hydrogen bonds : bond 0.03618 / 2.55 ( 410) hydrogen bonds : angle 4.51920 / 3.25 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.313 Fit side-chains REVERT: R 184 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7107 (mp) REVERT: R 186 MET cc_start: 0.7722 (mmt) cc_final: 0.7424 (mmt) REVERT: R 204 GLN cc_start: 0.6803 (mt0) cc_final: 0.5697 (pt0) REVERT: R 213 ARG cc_start: 0.6326 (mmt180) cc_final: 0.3729 (ptt-90) REVERT: R 333 ARG cc_start: 0.6831 (ttm170) cc_final: 0.5794 (ttm-80) REVERT: R 380 TYR cc_start: 0.7451 (m-80) cc_final: 0.7163 (m-80) REVERT: B 118 ASP cc_start: 0.8028 (p0) cc_final: 0.7551 (p0) REVERT: B 137 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7520 (tpp-160) REVERT: B 220 GLN cc_start: 0.7484 (mt0) cc_final: 0.7253 (mt0) REVERT: B 258 ASP cc_start: 0.8486 (t0) cc_final: 0.7977 (t0) REVERT: B 325 MET cc_start: 0.8314 (tpp) cc_final: 0.7851 (tpp) REVERT: E 30 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8212 (t) REVERT: E 116 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6734 (t) REVERT: E 146 SER cc_start: 0.8549 (t) cc_final: 0.8244 (p) REVERT: A 20 ASP cc_start: 0.7589 (t0) cc_final: 0.7300 (m-30) REVERT: A 327 ASP cc_start: 0.5429 (OUTLIER) cc_final: 0.5068 (m-30) outliers start: 25 outliers final: 17 residues processed: 141 average time/residue: 0.0935 time to fit residues: 18.4410 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143297 restraints weight = 9222.765| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.93 r_work: 0.3592 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8748 Z= 0.159 Angle : 0.615 7.735 11886 Z= 0.310 Chirality : 0.044 0.205 1374 Planarity : 0.004 0.082 1495 Dihedral : 4.630 39.933 1217 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.36 % Allowed : 14.33 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.68 (0.26), residues: 1097 helix: 1.69 (0.28), residues: 360 sheet: -0.86 (0.31), residues: 287 loop : -1.97 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 57 TYR 0.012 0.001 TYR E 178 PHE 0.016 0.001 PHE E 27 TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 8746) covalent geometry : angle 0.61296 / 0.31 (11882) SS BOND : bond 0.00851 / 0.44 ( 2) SS BOND : angle 2.55541 / 1.41 ( 4) hydrogen bonds : bond 0.03699 / 2.61 ( 410) hydrogen bonds : angle 4.50607 / 3.24 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.317 Fit side-chains REVERT: R 184 LEU cc_start: 0.7573 (tt) cc_final: 0.7097 (mp) REVERT: R 196 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.5643 (mp10) REVERT: R 204 GLN cc_start: 0.6613 (mt0) cc_final: 0.5561 (pt0) REVERT: R 207 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.5235 (m-70) REVERT: R 213 ARG cc_start: 0.6250 (mmt180) cc_final: 0.3628 (ptt-90) REVERT: R 333 ARG cc_start: 0.6802 (ttm170) cc_final: 0.5785 (ttm-80) REVERT: R 380 TYR cc_start: 0.7490 (m-80) cc_final: 0.7218 (m-80) REVERT: B 118 ASP cc_start: 0.8056 (p0) cc_final: 0.7593 (p0) REVERT: B 137 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7489 (tpp-160) REVERT: B 258 ASP cc_start: 0.8478 (t0) cc_final: 0.7917 (t0) REVERT: B 325 MET cc_start: 0.8321 (tpp) cc_final: 0.7826 (tpp) REVERT: E 30 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8092 (t) REVERT: E 116 THR cc_start: 0.6960 (OUTLIER) cc_final: 0.6675 (t) REVERT: E 146 SER cc_start: 0.8465 (t) cc_final: 0.8231 (p) REVERT: E 180 MET cc_start: 0.7805 (ptm) cc_final: 0.7585 (ptm) REVERT: A 20 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: A 327 ASP cc_start: 0.5189 (OUTLIER) cc_final: 0.4788 (m-30) outliers start: 30 outliers final: 18 residues processed: 137 average time/residue: 0.0890 time to fit residues: 17.2004 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.0030 chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 196 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143319 restraints weight = 9168.441| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.91 r_work: 0.3590 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8748 Z= 0.157 Angle : 0.616 8.111 11886 Z= 0.310 Chirality : 0.044 0.225 1374 Planarity : 0.004 0.082 1495 Dihedral : 4.657 39.968 1217 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.92 % Allowed : 14.78 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.55 (0.26), residues: 1097 helix: 1.77 (0.28), residues: 360 sheet: -0.77 (0.31), residues: 287 loop : -1.89 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.012 0.001 TYR E 178 PHE 0.016 0.001 PHE E 27 TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8746) covalent geometry : angle 0.61425 / 0.31 (11882) SS BOND : bond 0.00791 / 0.40 ( 2) SS BOND : angle 2.38828 / 1.32 ( 4) hydrogen bonds : bond 0.03661 / 2.58 ( 410) hydrogen bonds : angle 4.43349 / 3.20 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.327 Fit side-chains REVERT: R 184 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7035 (mp) REVERT: R 186 MET cc_start: 0.7744 (mmt) cc_final: 0.7438 (mmt) REVERT: R 194 VAL cc_start: 0.6142 (OUTLIER) cc_final: 0.5927 (m) REVERT: R 196 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.5476 (mp10) REVERT: R 204 GLN cc_start: 0.6578 (mt0) cc_final: 0.5452 (pt0) REVERT: R 207 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6093 (m-70) REVERT: R 213 ARG cc_start: 0.6259 (mmt180) cc_final: 0.3639 (ptt-90) REVERT: R 333 ARG cc_start: 0.6782 (ttm170) cc_final: 0.5779 (ttm-80) REVERT: R 380 TYR cc_start: 0.7474 (m-80) cc_final: 0.7189 (m-80) REVERT: B 118 ASP cc_start: 0.8076 (p0) cc_final: 0.7610 (p0) REVERT: B 137 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7503 (tpp-160) REVERT: B 220 GLN cc_start: 0.7551 (mt0) cc_final: 0.7315 (mt0) REVERT: B 325 MET cc_start: 0.8306 (tpp) cc_final: 0.7800 (tpp) REVERT: E 30 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8087 (t) REVERT: E 146 SER cc_start: 0.8500 (t) cc_final: 0.8277 (p) REVERT: A 20 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: A 327 ASP cc_start: 0.5227 (OUTLIER) cc_final: 0.4908 (m-30) REVERT: L 15 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6392 (ptp) outliers start: 35 outliers final: 25 residues processed: 138 average time/residue: 0.0852 time to fit residues: 16.9093 Evaluate side-chains 154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147418 restraints weight = 9201.536| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.90 r_work: 0.3606 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8748 Z= 0.136 Angle : 0.596 8.306 11886 Z= 0.300 Chirality : 0.043 0.243 1374 Planarity : 0.004 0.078 1495 Dihedral : 4.569 38.740 1217 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.44 (0.26), residues: 1097 helix: 1.84 (0.28), residues: 361 sheet: -0.70 (0.31), residues: 285 loop : -1.81 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.016 0.001 TYR A 285 PHE 0.015 0.001 PHE E 27 TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8746) covalent geometry : angle 0.59465 / 0.30 (11882) SS BOND : bond 0.00698 / 0.35 ( 2) SS BOND : angle 2.11940 / 1.17 ( 4) hydrogen bonds : bond 0.03533 / 2.49 ( 410) hydrogen bonds : angle 4.35898 / 3.15 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: R 184 LEU cc_start: 0.7568 (tt) cc_final: 0.7096 (mp) REVERT: R 186 MET cc_start: 0.7707 (mmt) cc_final: 0.7404 (mmt) REVERT: R 194 VAL cc_start: 0.6125 (OUTLIER) cc_final: 0.5907 (m) REVERT: R 204 GLN cc_start: 0.6426 (mt0) cc_final: 0.6125 (mm-40) REVERT: R 207 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6421 (m-70) REVERT: R 213 ARG cc_start: 0.6206 (mmt180) cc_final: 0.3581 (ptt-90) REVERT: R 333 ARG cc_start: 0.6592 (ttm170) cc_final: 0.5567 (ttm-80) REVERT: B 118 ASP cc_start: 0.7950 (p0) cc_final: 0.7460 (p0) REVERT: B 137 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7510 (tpp-160) REVERT: B 156 GLN cc_start: 0.8300 (mt0) cc_final: 0.8056 (mt0) REVERT: B 220 GLN cc_start: 0.7695 (mt0) cc_final: 0.7450 (mt0) REVERT: B 325 MET cc_start: 0.8316 (tpp) cc_final: 0.7814 (tpp) REVERT: E 30 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8099 (t) REVERT: E 43 LYS cc_start: 0.7399 (mmtp) cc_final: 0.7143 (mmtm) REVERT: E 146 SER cc_start: 0.8504 (t) cc_final: 0.8304 (p) REVERT: A 20 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: A 327 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.5043 (m-30) outliers start: 29 outliers final: 20 residues processed: 144 average time/residue: 0.0851 time to fit residues: 17.6016 Evaluate side-chains 146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 90 ASN R 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.186496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148403 restraints weight = 9035.467| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.90 r_work: 0.3649 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8748 Z= 0.108 Angle : 0.583 10.164 11886 Z= 0.291 Chirality : 0.043 0.238 1374 Planarity : 0.004 0.073 1495 Dihedral : 4.340 35.826 1217 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.14 % Allowed : 15.90 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.29 (0.26), residues: 1097 helix: 1.94 (0.28), residues: 362 sheet: -0.68 (0.30), residues: 288 loop : -1.67 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.031 0.001 TYR R 380 PHE 0.015 0.001 PHE A 49 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8746) covalent geometry : angle 0.58212 / 0.29 (11882) SS BOND : bond 0.00599 / 0.30 ( 2) SS BOND : angle 1.81245 / 1.01 ( 4) hydrogen bonds : bond 0.03281 / 2.31 ( 410) hydrogen bonds : angle 4.19492 / 3.03 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: R 184 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7137 (mp) REVERT: R 186 MET cc_start: 0.7827 (mmt) cc_final: 0.7527 (mmt) REVERT: R 207 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6785 (m-70) REVERT: R 333 ARG cc_start: 0.6417 (ttm170) cc_final: 0.5316 (ttm-80) REVERT: B 118 ASP cc_start: 0.7829 (p0) cc_final: 0.7315 (p0) REVERT: B 137 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7484 (tpp-160) REVERT: B 325 MET cc_start: 0.8272 (tpp) cc_final: 0.7867 (tpp) REVERT: E 30 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8022 (t) REVERT: E 43 LYS cc_start: 0.7320 (mmtp) cc_final: 0.7055 (mmtm) REVERT: E 116 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6580 (t) REVERT: A 20 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 327 ASP cc_start: 0.5277 (OUTLIER) cc_final: 0.4904 (m-30) outliers start: 28 outliers final: 17 residues processed: 138 average time/residue: 0.0849 time to fit residues: 16.8324 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145649 restraints weight = 9266.932| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.53 r_work: 0.3629 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8748 Z= 0.156 Angle : 0.629 8.946 11886 Z= 0.313 Chirality : 0.044 0.241 1374 Planarity : 0.004 0.083 1495 Dihedral : 4.512 35.945 1217 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.02 % Allowed : 15.57 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.32 (0.26), residues: 1097 helix: 1.91 (0.28), residues: 363 sheet: -0.67 (0.31), residues: 286 loop : -1.70 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.013 0.001 TYR E 178 PHE 0.015 0.001 PHE E 27 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8746) covalent geometry : angle 0.62761 / 0.31 (11882) SS BOND : bond 0.00702 / 0.35 ( 2) SS BOND : angle 2.04311 / 1.12 ( 4) hydrogen bonds : bond 0.03594 / 2.54 ( 410) hydrogen bonds : angle 4.32569 / 3.14 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: R 333 ARG cc_start: 0.6653 (ttm170) cc_final: 0.5681 (ttm-80) REVERT: B 118 ASP cc_start: 0.8015 (p0) cc_final: 0.7480 (p0) REVERT: B 137 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7633 (tpp-160) REVERT: B 220 GLN cc_start: 0.7942 (mt0) cc_final: 0.7666 (mt0) REVERT: B 325 MET cc_start: 0.8361 (tpp) cc_final: 0.7927 (tpp) REVERT: E 30 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8076 (t) REVERT: E 43 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7318 (mmtm) REVERT: A 20 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: A 327 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5370 (m-30) outliers start: 27 outliers final: 19 residues processed: 139 average time/residue: 0.0824 time to fit residues: 16.5019 Evaluate side-chains 145 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain L residue 15 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 103 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.184782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146563 restraints weight = 9268.340| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.90 r_work: 0.3656 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8748 Z= 0.101 Angle : 0.583 9.049 11886 Z= 0.290 Chirality : 0.042 0.234 1374 Planarity : 0.004 0.072 1495 Dihedral : 4.212 31.185 1217 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.13 % Allowed : 16.57 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.10 (0.26), residues: 1097 helix: 2.12 (0.28), residues: 362 sheet: -0.61 (0.30), residues: 288 loop : -1.54 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.012 0.001 TYR E 178 PHE 0.016 0.001 PHE A 49 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 8746) covalent geometry : angle 0.58240 / 0.29 (11882) SS BOND : bond 0.00567 / 0.29 ( 2) SS BOND : angle 1.74509 / 0.98 ( 4) hydrogen bonds : bond 0.03125 / 2.21 ( 410) hydrogen bonds : angle 4.08766 / 2.96 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: R 134 MET cc_start: 0.6912 (mmm) cc_final: 0.6685 (mmm) REVERT: R 184 LEU cc_start: 0.7824 (tt) cc_final: 0.7342 (mp) REVERT: R 333 ARG cc_start: 0.6398 (ttm170) cc_final: 0.5278 (ttm-80) REVERT: B 137 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7513 (tpp-160) REVERT: B 164 THR cc_start: 0.8456 (p) cc_final: 0.8095 (m) REVERT: B 205 ASP cc_start: 0.7653 (p0) cc_final: 0.7266 (t0) REVERT: B 325 MET cc_start: 0.8235 (tpp) cc_final: 0.7814 (tpp) REVERT: E 30 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8064 (t) REVERT: E 43 LYS cc_start: 0.7482 (mmtp) cc_final: 0.7245 (mmtm) REVERT: E 57 THR cc_start: 0.8257 (m) cc_final: 0.7930 (p) REVERT: E 180 MET cc_start: 0.7680 (ptm) cc_final: 0.7367 (ptt) REVERT: A 20 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: A 327 ASP cc_start: 0.5376 (OUTLIER) cc_final: 0.5057 (m-30) outliers start: 19 outliers final: 15 residues processed: 129 average time/residue: 0.0819 time to fit residues: 15.3638 Evaluate side-chains 131 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 0.0470 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.0000 chunk 29 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 166 GLN R 196 GLN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.185002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146794 restraints weight = 9181.535| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.90 r_work: 0.3660 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8748 Z= 0.104 Angle : 0.589 10.213 11886 Z= 0.291 Chirality : 0.042 0.281 1374 Planarity : 0.004 0.074 1495 Dihedral : 4.150 31.225 1217 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.13 % Allowed : 17.58 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.03 (0.26), residues: 1097 helix: 2.24 (0.28), residues: 363 sheet: -0.55 (0.30), residues: 283 loop : -1.48 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.011 0.001 TYR E 178 PHE 0.016 0.001 PHE A 49 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 8746) covalent geometry : angle 0.58824 / 0.29 (11882) SS BOND : bond 0.00552 / 0.28 ( 2) SS BOND : angle 1.64002 / 0.91 ( 4) hydrogen bonds : bond 0.03270 / 2.30 ( 410) hydrogen bonds : angle 4.06574 / 2.95 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.87 seconds wall clock time: 39 minutes 27.92 seconds (2367.92 seconds total)