Starting phenix.real_space_refine on Tue Mar 3 20:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xow_33361/03_2026/7xow_33361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xow_33361/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_2026/7xow_33361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_2026/7xow_33361.map" model { file = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_2026/7xow_33361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xow_33361/03_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-5986/lib/python3.9/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: 1.80, per 1000 atoms: 0.21 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: 0.65 Conformation dependent library (CDL) restraints added in 322.4 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: 1.13 Time building geometry restraints manager: 0.89 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.720 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 covalent geometry : bond 0.00465 ( 8746) covalent geometry : angle 0.85659 (11882) SS BOND : bond 0.00517 ( 2) SS BOND : angle 1.56428 ( 4) hydrogen bonds : bond 0.14300 ( 410) hydrogen bonds : angle 6.50579 ( 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 : 0.293 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: 0.1187 time to fit residues: 26.5132 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 : 0.250 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4204 r_free = 0.4204 target = 0.190265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151972 restraints weight = 9077.703| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.87 r_work: 0.3650 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8748 Z= 0.119 Angle : 0.589 8.311 11886 Z= 0.300 Chirality : 0.043 0.152 1374 Planarity : 0.005 0.082 1495 Dihedral : 4.693 38.831 1219 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 1.68 % Allowed : 10.19 % 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: -1.50 (0.25), residues: 1097 helix: 0.96 (0.28), residues: 366 sheet: -1.28 (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 0.022 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 covalent geometry : bond 0.00256 ( 8746) covalent geometry : angle 0.58770 (11882) SS BOND : bond 0.00797 ( 2) SS BOND : angle 2.41429 ( 4) hydrogen bonds : bond 0.03708 ( 410) hydrogen bonds : angle 4.90039 ( 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 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.304 Fit side-chains REVERT: R 207 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.5088 (m-70) REVERT: R 213 ARG cc_start: 0.6092 (mmt180) cc_final: 0.3518 (ptt-90) REVERT: R 333 ARG cc_start: 0.6648 (ttm170) cc_final: 0.5678 (ttm-80) REVERT: R 380 TYR cc_start: 0.7317 (m-80) cc_final: 0.6936 (m-80) REVERT: R 398 ARG cc_start: 0.6814 (mmt90) cc_final: 0.6418 (mmp80) REVERT: B 220 GLN cc_start: 0.7741 (mt0) cc_final: 0.7540 (mt0) REVERT: B 258 ASP cc_start: 0.8435 (t0) cc_final: 0.7821 (t0) REVERT: B 325 MET cc_start: 0.8230 (tpp) cc_final: 0.7797 (tpp) REVERT: A 242 MET cc_start: 0.7345 (tpp) cc_final: 0.6302 (tpp) REVERT: A 305 LYS cc_start: 0.6766 (ttpp) cc_final: 0.6488 (tppt) REVERT: A 339 LYS cc_start: 0.7150 (tttt) cc_final: 0.6947 (tttp) outliers start: 15 outliers final: 8 residues processed: 158 average time/residue: 0.0911 time to fit residues: 19.8293 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 : 0.237 ------------------------------------------------------------------------------- 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: 4.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144216 restraints weight = 9191.689| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.80 r_work: 0.3448 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.1720 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= 0.122 Angle : 0.588 8.443 11886 Z= 0.297 Chirality : 0.043 0.175 1374 Planarity : 0.004 0.080 1495 Dihedral : 4.615 37.592 1219 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 2.80 % Allowed : 12.32 % 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: -0.98 (0.26), residues: 1097 helix: 1.41 (0.28), residues: 367 sheet: -1.03 (0.30), residues: 285 loop : -2.18 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.019 0.001 TYR A 285 PHE 0.014 0.001 PHE A 49 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8746) covalent geometry : angle 0.58631 (11882) SS BOND : bond 0.00480 ( 2) SS BOND : angle 2.58954 ( 4) hydrogen bonds : bond 0.03499 ( 410) hydrogen bonds : angle 4.57081 ( 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 166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.298 Fit side-chains REVERT: R 184 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6773 (mp) REVERT: R 196 GLN cc_start: 0.5897 (OUTLIER) cc_final: 0.5573 (mp10) REVERT: R 213 ARG cc_start: 0.6003 (mmt180) cc_final: 0.3373 (ptt-90) REVERT: R 244 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5104 (mp0) REVERT: R 333 ARG cc_start: 0.6513 (ttm170) cc_final: 0.5458 (ttm-80) REVERT: R 380 TYR cc_start: 0.6983 (m-80) cc_final: 0.6576 (m-80) REVERT: R 398 ARG cc_start: 0.6493 (mmt90) cc_final: 0.6169 (mmp80) REVERT: B 67 SER cc_start: 0.8179 (t) cc_final: 0.7909 (m) REVERT: B 137 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7014 (tpp-160) REVERT: B 258 ASP cc_start: 0.8154 (t0) cc_final: 0.7343 (t0) REVERT: B 325 MET cc_start: 0.7903 (tpp) cc_final: 0.7349 (tpp) REVERT: E 19 LYS cc_start: 0.7829 (tttt) cc_final: 0.7624 (tttm) REVERT: E 30 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8116 (t) REVERT: E 126 ILE cc_start: 0.7783 (mp) cc_final: 0.7468 (mt) REVERT: E 146 SER cc_start: 0.8454 (t) cc_final: 0.8164 (p) REVERT: E 177 ILE cc_start: 0.8238 (pt) cc_final: 0.8008 (pt) REVERT: A 196 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7717 (ttm-80) REVERT: A 305 LYS cc_start: 0.6399 (ttpp) cc_final: 0.6195 (tppt) REVERT: A 327 ASP cc_start: 0.5129 (OUTLIER) cc_final: 0.4805 (m-30) REVERT: L 15 MET cc_start: 0.6827 (ptp) cc_final: 0.6291 (mtp) outliers start: 25 outliers final: 14 residues processed: 152 average time/residue: 0.0843 time to fit residues: 17.9941 Evaluate side-chains 152 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 201 THR 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 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: 1.9990 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 204 GLN A 321 HIS A 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138875 restraints weight = 9341.628| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.92 r_work: 0.3581 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8748 Z= 0.186 Angle : 0.643 7.773 11886 Z= 0.325 Chirality : 0.045 0.195 1374 Planarity : 0.005 0.090 1495 Dihedral : 4.813 41.183 1217 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.14 % Allowed : 13.55 % Favored : 83.31 % 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: -0.92 (0.26), residues: 1097 helix: 1.41 (0.28), residues: 366 sheet: -0.99 (0.30), residues: 297 loop : -2.11 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.014 0.002 TYR E 178 PHE 0.018 0.002 PHE E 27 TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8746) covalent geometry : angle 0.64079 (11882) SS BOND : bond 0.00974 ( 2) SS BOND : angle 2.93932 ( 4) hydrogen bonds : bond 0.03908 ( 410) hydrogen bonds : angle 4.65732 ( 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 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.247 Fit side-chains REVERT: R 213 ARG cc_start: 0.6475 (mmt180) cc_final: 0.3852 (ptt-90) REVERT: R 333 ARG cc_start: 0.6857 (ttm170) cc_final: 0.5799 (ttm-80) REVERT: R 380 TYR cc_start: 0.7429 (m-80) cc_final: 0.7132 (m-80) REVERT: B 118 ASP cc_start: 0.8101 (p0) cc_final: 0.7633 (p0) REVERT: B 119 ASN cc_start: 0.8324 (m-40) cc_final: 0.8123 (m-40) REVERT: B 137 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7486 (tpp-160) REVERT: B 258 ASP cc_start: 0.8454 (t0) cc_final: 0.7938 (t0) REVERT: B 325 MET cc_start: 0.8297 (tpp) cc_final: 0.7812 (tpp) REVERT: E 30 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8083 (t) REVERT: E 116 THR cc_start: 0.6911 (OUTLIER) cc_final: 0.6621 (t) REVERT: E 146 SER cc_start: 0.8489 (t) cc_final: 0.8238 (p) REVERT: E 177 ILE cc_start: 0.8448 (pt) cc_final: 0.8208 (pt) REVERT: A 20 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: A 242 MET cc_start: 0.7236 (tpp) cc_final: 0.6300 (tpp) REVERT: A 305 LYS cc_start: 0.6765 (ttpp) cc_final: 0.6543 (tppt) REVERT: A 327 ASP cc_start: 0.5456 (OUTLIER) cc_final: 0.5083 (m-30) outliers start: 28 outliers final: 18 residues processed: 147 average time/residue: 0.0864 time to fit residues: 17.5912 Evaluate side-chains 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 93 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 20 ASP 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145975 restraints weight = 9146.004| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.89 r_work: 0.3621 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8748 Z= 0.126 Angle : 0.583 7.747 11886 Z= 0.294 Chirality : 0.043 0.195 1374 Planarity : 0.004 0.079 1495 Dihedral : 4.565 38.302 1217 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.80 % Allowed : 15.01 % Favored : 82.19 % 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: -0.58 (0.26), residues: 1097 helix: 1.73 (0.28), residues: 362 sheet: -0.82 (0.30), residues: 285 loop : -1.88 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 396 TYR 0.011 0.001 TYR E 178 PHE 0.014 0.001 PHE A 49 TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8746) covalent geometry : angle 0.58133 (11882) SS BOND : bond 0.00744 ( 2) SS BOND : angle 2.34797 ( 4) hydrogen bonds : bond 0.03474 ( 410) hydrogen bonds : angle 4.42287 ( 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 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.319 Fit side-chains REVERT: R 184 LEU cc_start: 0.7609 (tt) cc_final: 0.7111 (mp) REVERT: R 186 MET cc_start: 0.7695 (mmt) cc_final: 0.7425 (mmt) REVERT: R 204 GLN cc_start: 0.6571 (mt0) cc_final: 0.5455 (pt0) REVERT: R 207 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.4955 (m-70) REVERT: R 213 ARG cc_start: 0.6325 (mmt180) cc_final: 0.3715 (ptt-90) REVERT: R 333 ARG cc_start: 0.6561 (ttm170) cc_final: 0.5542 (ttm-80) REVERT: R 380 TYR cc_start: 0.7502 (m-80) cc_final: 0.7220 (m-80) REVERT: B 118 ASP cc_start: 0.8038 (p0) cc_final: 0.7553 (p0) REVERT: B 137 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7500 (tpp-160) REVERT: B 258 ASP cc_start: 0.8363 (t0) cc_final: 0.7799 (t0) REVERT: B 325 MET cc_start: 0.8326 (tpp) cc_final: 0.7840 (tpp) REVERT: E 30 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8100 (t) REVERT: E 116 THR cc_start: 0.6935 (OUTLIER) cc_final: 0.6634 (t) REVERT: E 146 SER cc_start: 0.8482 (t) cc_final: 0.8218 (p) REVERT: E 177 ILE cc_start: 0.8400 (pt) cc_final: 0.8146 (pt) REVERT: A 20 ASP cc_start: 0.7580 (t0) cc_final: 0.7295 (m-30) REVERT: A 305 LYS cc_start: 0.6773 (ttpp) cc_final: 0.6570 (tppt) REVERT: A 327 ASP cc_start: 0.5178 (OUTLIER) cc_final: 0.4818 (m-30) REVERT: L 15 MET cc_start: 0.7144 (ptp) cc_final: 0.6449 (mtp) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.0853 time to fit residues: 16.6391 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 207 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145352 restraints weight = 9120.411| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.90 r_work: 0.3613 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8748 Z= 0.140 Angle : 0.598 7.969 11886 Z= 0.301 Chirality : 0.043 0.220 1374 Planarity : 0.004 0.080 1495 Dihedral : 4.572 37.712 1217 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.81 % Allowed : 15.01 % Favored : 81.19 % 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: -0.48 (0.26), residues: 1097 helix: 1.79 (0.28), residues: 361 sheet: -0.75 (0.31), residues: 287 loop : -1.80 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.011 0.001 TYR E 178 PHE 0.015 0.001 PHE E 27 TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8746) covalent geometry : angle 0.59668 (11882) SS BOND : bond 0.00797 ( 2) SS BOND : angle 2.31621 ( 4) hydrogen bonds : bond 0.03519 ( 410) hydrogen bonds : angle 4.34443 ( 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 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.312 Fit side-chains REVERT: R 90 ASN cc_start: 0.6831 (m110) cc_final: 0.6562 (m-40) REVERT: R 184 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7081 (mp) REVERT: R 204 GLN cc_start: 0.6487 (mt0) cc_final: 0.5295 (pt0) REVERT: R 207 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.5994 (m-70) REVERT: R 213 ARG cc_start: 0.6338 (mmt180) cc_final: 0.3614 (ptt-90) REVERT: R 333 ARG cc_start: 0.6575 (ttm170) cc_final: 0.5554 (ttm-80) REVERT: R 380 TYR cc_start: 0.7515 (m-80) cc_final: 0.7271 (m-80) REVERT: B 118 ASP cc_start: 0.7960 (p0) cc_final: 0.7498 (p0) REVERT: B 137 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7500 (tpp-160) REVERT: B 156 GLN cc_start: 0.8312 (mt0) cc_final: 0.8089 (mt0) REVERT: B 325 MET cc_start: 0.8331 (tpp) cc_final: 0.7908 (tpp) REVERT: E 30 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8089 (t) REVERT: E 116 THR cc_start: 0.6917 (OUTLIER) cc_final: 0.6614 (t) REVERT: E 146 SER cc_start: 0.8462 (t) cc_final: 0.8234 (p) REVERT: E 177 ILE cc_start: 0.8389 (pt) cc_final: 0.8130 (pt) REVERT: E 180 MET cc_start: 0.7772 (ptm) cc_final: 0.7523 (ptm) REVERT: A 20 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: A 327 ASP cc_start: 0.5131 (OUTLIER) cc_final: 0.4720 (m-30) REVERT: L 15 MET cc_start: 0.7028 (ptp) cc_final: 0.6259 (mtp) outliers start: 34 outliers final: 20 residues processed: 152 average time/residue: 0.0780 time to fit residues: 17.2204 Evaluate side-chains 148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 20 LEU 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 201 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 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 = 0.184211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145532 restraints weight = 9268.691| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.95 r_work: 0.3646 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8748 Z= 0.111 Angle : 0.579 9.900 11886 Z= 0.289 Chirality : 0.043 0.237 1374 Planarity : 0.004 0.072 1495 Dihedral : 4.386 34.935 1217 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.02 % Allowed : 15.68 % 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: -0.28 (0.26), residues: 1097 helix: 1.96 (0.28), residues: 362 sheet: -0.61 (0.31), residues: 283 loop : -1.72 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.014 0.001 TYR A 285 PHE 0.014 0.001 PHE A 49 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8746) covalent geometry : angle 0.57785 (11882) SS BOND : bond 0.00743 ( 2) SS BOND : angle 2.05779 ( 4) hydrogen bonds : bond 0.03278 ( 410) hydrogen bonds : angle 4.17438 ( 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 149 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.340 Fit side-chains REVERT: R 184 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7275 (mp) REVERT: R 207 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6470 (m-70) REVERT: R 333 ARG cc_start: 0.6398 (ttm170) cc_final: 0.5306 (ttm-80) REVERT: B 118 ASP cc_start: 0.7844 (p0) cc_final: 0.7358 (p0) REVERT: B 137 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7488 (tpp-160) REVERT: B 164 THR cc_start: 0.8466 (p) cc_final: 0.8164 (m) REVERT: B 325 MET cc_start: 0.8318 (tpp) cc_final: 0.7896 (tpp) REVERT: E 30 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (t) REVERT: E 43 LYS cc_start: 0.7328 (mmtp) cc_final: 0.7057 (mmtm) REVERT: E 116 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6636 (t) REVERT: E 146 SER cc_start: 0.8519 (t) cc_final: 0.8288 (p) REVERT: E 177 ILE cc_start: 0.8305 (pt) cc_final: 0.8039 (pt) REVERT: E 180 MET cc_start: 0.7694 (ptm) cc_final: 0.7438 (ptm) REVERT: A 20 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 327 ASP cc_start: 0.5088 (OUTLIER) cc_final: 0.4752 (m-30) REVERT: L 15 MET cc_start: 0.7210 (ptp) cc_final: 0.6294 (mtp) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 0.0806 time to fit residues: 15.8862 Evaluate side-chains 142 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 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 201 THR 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 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: 0.7980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 0.0670 chunk 75 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.185286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147888 restraints weight = 9067.480| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.82 r_work: 0.3647 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8748 Z= 0.108 Angle : 0.587 12.755 11886 Z= 0.290 Chirality : 0.043 0.318 1374 Planarity : 0.004 0.075 1495 Dihedral : 4.287 31.829 1217 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.91 % Allowed : 16.24 % Favored : 80.85 % 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: -0.18 (0.26), residues: 1097 helix: 2.05 (0.28), residues: 362 sheet: -0.62 (0.31), residues: 287 loop : -1.61 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.035 0.001 TYR R 380 PHE 0.015 0.001 PHE A 49 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8746) covalent geometry : angle 0.58565 (11882) SS BOND : bond 0.00539 ( 2) SS BOND : angle 2.01178 ( 4) hydrogen bonds : bond 0.03374 ( 410) hydrogen bonds : angle 4.12852 ( 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 148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.320 Fit side-chains REVERT: R 184 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7383 (mp) REVERT: R 333 ARG cc_start: 0.6433 (ttm170) cc_final: 0.5357 (ttm-80) REVERT: R 380 TYR cc_start: 0.7626 (m-80) cc_final: 0.7251 (m-80) REVERT: B 137 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7542 (tpp-160) REVERT: B 164 THR cc_start: 0.8422 (p) cc_final: 0.8097 (m) REVERT: B 325 MET cc_start: 0.8303 (tpp) cc_final: 0.7872 (tpp) REVERT: E 30 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8084 (t) REVERT: E 43 LYS cc_start: 0.7538 (mmtp) cc_final: 0.7271 (mmtm) REVERT: E 116 THR cc_start: 0.6908 (OUTLIER) cc_final: 0.6595 (t) REVERT: E 146 SER cc_start: 0.8537 (t) cc_final: 0.8307 (p) REVERT: E 177 ILE cc_start: 0.8379 (pt) cc_final: 0.8110 (pt) REVERT: E 180 MET cc_start: 0.7659 (ptm) cc_final: 0.7361 (ptm) REVERT: A 20 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: A 327 ASP cc_start: 0.5078 (OUTLIER) cc_final: 0.4727 (m-30) outliers start: 26 outliers final: 17 residues processed: 138 average time/residue: 0.0757 time to fit residues: 15.1256 Evaluate side-chains 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 20 LEU 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 201 THR Chi-restraints excluded: chain E residue 204 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143266 restraints weight = 9310.868| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.52 r_work: 0.3600 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8748 Z= 0.205 Angle : 0.680 10.375 11886 Z= 0.340 Chirality : 0.046 0.276 1374 Planarity : 0.004 0.083 1495 Dihedral : 4.781 38.921 1217 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.80 % Allowed : 16.57 % Favored : 80.63 % 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: -0.40 (0.26), residues: 1097 helix: 1.77 (0.28), residues: 362 sheet: -0.64 (0.31), residues: 296 loop : -1.76 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.025 0.002 TYR R 380 PHE 0.018 0.002 PHE E 27 TRP 0.012 0.001 TRP E 47 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8746) covalent geometry : angle 0.67867 (11882) SS BOND : bond 0.00881 ( 2) SS BOND : angle 2.51828 ( 4) hydrogen bonds : bond 0.04007 ( 410) hydrogen bonds : angle 4.50756 ( 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 149 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.325 Fit side-chains REVERT: R 184 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7392 (mp) REVERT: R 204 GLN cc_start: 0.6665 (mt0) cc_final: 0.6384 (mm-40) REVERT: R 213 ARG cc_start: 0.6527 (mmt180) cc_final: 0.3872 (ptt-90) REVERT: R 333 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6012 (ttm-80) REVERT: R 380 TYR cc_start: 0.7715 (m-80) cc_final: 0.7422 (m-80) REVERT: B 118 ASP cc_start: 0.8299 (p0) cc_final: 0.7816 (p0) REVERT: B 137 ARG cc_start: 0.8437 (mmm160) cc_final: 0.7733 (tpp-160) REVERT: B 156 GLN cc_start: 0.8600 (mt0) cc_final: 0.8396 (mt0) REVERT: B 205 ASP cc_start: 0.7941 (p0) cc_final: 0.7560 (t0) REVERT: B 325 MET cc_start: 0.8468 (tpp) cc_final: 0.7979 (tpp) REVERT: E 30 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8163 (t) REVERT: E 43 LYS cc_start: 0.7496 (mmtp) cc_final: 0.7243 (mmtm) REVERT: E 116 THR cc_start: 0.7064 (OUTLIER) cc_final: 0.6735 (t) REVERT: E 146 SER cc_start: 0.8544 (t) cc_final: 0.8342 (p) REVERT: E 177 ILE cc_start: 0.8540 (pt) cc_final: 0.8274 (pt) REVERT: E 180 MET cc_start: 0.7925 (ptm) cc_final: 0.7546 (ptm) REVERT: A 20 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: A 327 ASP cc_start: 0.5607 (OUTLIER) cc_final: 0.5357 (m-30) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.0873 time to fit residues: 17.0376 Evaluate side-chains 141 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145567 restraints weight = 9261.889| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.89 r_work: 0.3616 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2757 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= 0.118 Angle : 0.608 10.123 11886 Z= 0.302 Chirality : 0.043 0.265 1374 Planarity : 0.004 0.073 1495 Dihedral : 4.454 34.657 1217 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.35 % Allowed : 17.69 % Favored : 79.96 % 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: -0.19 (0.26), residues: 1097 helix: 2.05 (0.28), residues: 361 sheet: -0.71 (0.30), residues: 289 loop : -1.55 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.025 0.001 TYR R 380 PHE 0.015 0.001 PHE A 49 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8746) covalent geometry : angle 0.60683 (11882) SS BOND : bond 0.00676 ( 2) SS BOND : angle 2.19215 ( 4) hydrogen bonds : bond 0.03420 ( 410) hydrogen bonds : angle 4.24563 ( 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 132 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.387 Fit side-chains REVERT: R 184 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7448 (mp) REVERT: R 333 ARG cc_start: 0.6480 (ttm170) cc_final: 0.5377 (ttm-80) REVERT: R 380 TYR cc_start: 0.7623 (m-80) cc_final: 0.7345 (m-80) REVERT: B 22 ARG cc_start: 0.6546 (ttm170) cc_final: 0.5956 (ttm170) REVERT: B 118 ASP cc_start: 0.7790 (p0) cc_final: 0.7257 (p0) REVERT: B 137 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7497 (tpp-160) REVERT: B 164 THR cc_start: 0.8543 (p) cc_final: 0.8171 (m) REVERT: B 205 ASP cc_start: 0.7692 (p0) cc_final: 0.7426 (t0) REVERT: B 325 MET cc_start: 0.8343 (tpp) cc_final: 0.7905 (tpp) REVERT: E 30 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8074 (t) REVERT: E 43 LYS cc_start: 0.7434 (mmtp) cc_final: 0.7219 (mmtm) REVERT: E 82 GLN cc_start: 0.7164 (tp40) cc_final: 0.6855 (tp40) REVERT: E 116 THR cc_start: 0.6898 (OUTLIER) cc_final: 0.6576 (t) REVERT: E 146 SER cc_start: 0.8507 (t) cc_final: 0.8305 (p) REVERT: E 177 ILE cc_start: 0.8305 (pt) cc_final: 0.8039 (pt) REVERT: E 180 MET cc_start: 0.7703 (ptm) cc_final: 0.7372 (ptm) REVERT: A 20 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: A 327 ASP cc_start: 0.5483 (OUTLIER) cc_final: 0.5182 (m-30) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 0.0885 time to fit residues: 15.5549 Evaluate side-chains 126 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 64 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.186531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148898 restraints weight = 9068.527| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.84 r_work: 0.3659 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8748 Z= 0.104 Angle : 0.585 10.209 11886 Z= 0.290 Chirality : 0.042 0.256 1374 Planarity : 0.004 0.070 1495 Dihedral : 4.196 35.885 1217 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.79 % Allowed : 18.14 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1097 helix: 2.25 (0.28), residues: 360 sheet: -0.54 (0.31), residues: 282 loop : -1.47 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.025 0.001 TYR R 380 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 covalent geometry : bond 0.00227 ( 8746) covalent geometry : angle 0.58368 (11882) SS BOND : bond 0.00570 ( 2) SS BOND : angle 1.81377 ( 4) hydrogen bonds : bond 0.03168 ( 410) hydrogen bonds : angle 4.10762 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.58 seconds wall clock time: 39 minutes 19.65 seconds (2359.65 seconds total)