Starting phenix.real_space_refine on Tue Mar 3 20:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmv_30411/03_2026/7cmv_30411_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmv_30411/03_2026/7cmv_30411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cmv_30411/03_2026/7cmv_30411_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmv_30411/03_2026/7cmv_30411_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cmv_30411/03_2026/7cmv_30411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmv_30411/03_2026/7cmv_30411.map" } resolution = 2.7 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= 0.009 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 67 5.16 5 C 5575 2.51 5 N 1489 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 8775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2128 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'G6O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8775 At special positions: 0 Unit cell: (104.442, 129.792, 114.582, 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 67 16.00 O 1644 8.00 N 1489 7.00 C 5575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 347.6 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 41.0% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.816A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.265A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.118A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.068A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.832A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.623A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.795A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 removed outlier: 4.394A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.540A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.039A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 33 through 57 Processing helix chain 'R' and resid 62 through 82 removed outlier: 4.109A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'R' and resid 99 through 134 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 143 through 170 removed outlier: 3.557A pdb=" N ARG R 149 " --> pdb=" O SER R 145 " (cutoff:3.500A) Proline residue: R 167 - end of helix removed outlier: 3.515A pdb=" N PHE R 170 " --> pdb=" O CYS R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.917A pdb=" N ILE R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 223 Processing helix chain 'R' and resid 322 through 355 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 361 through 385 removed outlier: 3.691A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 387 through 400 removed outlier: 3.818A pdb=" N CYS R 400 " --> pdb=" O LYS R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.555A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.781A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.584A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.671A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.875A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.400A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.041A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.799A 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=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.764A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.501A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.896A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.896A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1275 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: 1.41 Time building geometry restraints manager: 0.91 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: 1470 1.32 - 1.44: 2418 1.44 - 1.57: 4969 1.57 - 1.69: 3 1.69 - 1.81: 95 Bond restraints: 8955 Sorted by residual: bond pdb=" C2 G6O R 500 " pdb=" C4 G6O R 500 " ideal model delta sigma weight residual 1.392 1.614 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1 G6O R 500 " pdb=" C3 G6O R 500 " ideal model delta sigma weight residual 1.392 1.593 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 G6O R 500 " pdb=" C6 G6O R 500 " ideal model delta sigma weight residual 1.393 1.200 0.193 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C10 G6O R 500 " pdb=" O2 G6O R 500 " ideal model delta sigma weight residual 1.426 1.259 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " ideal model delta sigma weight residual 1.357 1.231 0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 8950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 12106 3.27 - 6.54: 29 6.54 - 9.82: 2 9.82 - 13.09: 1 13.09 - 16.36: 1 Bond angle restraints: 12139 Sorted by residual: angle pdb=" C10 G6O R 500 " pdb=" O2 G6O R 500 " pdb=" C7 G6O R 500 " ideal model delta sigma weight residual 113.23 129.59 -16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " pdb=" C8 G6O R 500 " ideal model delta sigma weight residual 117.80 130.12 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C4 G6O R 500 " pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " ideal model delta sigma weight residual 117.00 126.76 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N HIS R 349 " pdb=" CA HIS R 349 " pdb=" C HIS R 349 " ideal model delta sigma weight residual 111.07 107.80 3.27 1.07e+00 8.73e-01 9.33e+00 angle pdb=" C THR R 348 " pdb=" N HIS R 349 " pdb=" CA HIS R 349 " ideal model delta sigma weight residual 120.44 124.03 -3.59 1.30e+00 5.92e-01 7.64e+00 ... (remaining 12134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4967 17.93 - 35.86: 300 35.86 - 53.79: 39 53.79 - 71.72: 15 71.72 - 89.64: 10 Dihedral angle restraints: 5331 sinusoidal: 2071 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 61.37 31.63 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU B 10 " pdb=" CG GLU B 10 " pdb=" CD GLU B 10 " pdb=" OE1 GLU B 10 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 869 0.027 - 0.053: 327 0.053 - 0.080: 99 0.080 - 0.107: 57 0.107 - 0.134: 41 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1390 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO E 75 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 349 " 0.007 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C HIS R 349 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS R 349 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 350 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 13 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ARG C 13 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG C 13 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS C 14 " 0.008 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 99 2.61 - 3.18: 7597 3.18 - 3.75: 13212 3.75 - 4.33: 18737 4.33 - 4.90: 32082 Nonbonded interactions: 71727 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR E 150 " pdb=" OE1 GLU E 153 " model vdw 2.091 3.040 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.161 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.162 3.120 nonbonded pdb=" OD1 ASP A 315 " pdb=" N THR A 316 " model vdw 2.207 3.120 ... (remaining 71722 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: 0.030 Set scattering table: 0.030 Process input model: 9.820 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: 0.010 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.222 8958 Z= 0.272 Angle : 0.487 16.359 12145 Z= 0.260 Chirality : 0.039 0.134 1393 Planarity : 0.002 0.056 1528 Dihedral : 12.439 89.644 3218 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.95 (0.26), residues: 1105 helix: 3.91 (0.25), residues: 374 sheet: 1.44 (0.31), residues: 269 loop : 0.65 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 219 TYR 0.004 0.000 TYR R 212 PHE 0.009 0.001 PHE R 345 TRP 0.019 0.001 TRP R 85 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 8955) covalent geometry : angle 0.48742 (12139) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.34567 ( 6) hydrogen bonds : bond 0.17735 ( 451) hydrogen bonds : angle 6.12406 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.319 Fit side-chains REVERT: B 19 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.6718 (ttm110) REVERT: B 47 THR cc_start: 0.8744 (t) cc_final: 0.8494 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.5910 time to fit residues: 110.8798 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 244 HIS B 62 HIS B 75 GLN B 175 GLN E 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126586 restraints weight = 9990.431| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.81 r_work: 0.3129 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8958 Z= 0.177 Angle : 0.614 10.050 12145 Z= 0.324 Chirality : 0.045 0.170 1393 Planarity : 0.004 0.049 1528 Dihedral : 4.261 23.317 1239 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.91 % Allowed : 8.42 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.30 (0.25), residues: 1105 helix: 3.23 (0.25), residues: 388 sheet: 1.20 (0.30), residues: 276 loop : 0.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.013 0.001 TYR R 383 PHE 0.017 0.002 PHE R 345 TRP 0.016 0.002 TRP B 99 HIS 0.007 0.002 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8955) covalent geometry : angle 0.61396 (12139) SS BOND : bond 0.00504 ( 3) SS BOND : angle 1.12728 ( 6) hydrogen bonds : bond 0.04559 ( 451) hydrogen bonds : angle 4.66013 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.241 Fit side-chains REVERT: A 26 ASP cc_start: 0.8152 (m-30) cc_final: 0.7886 (m-30) REVERT: A 312 LYS cc_start: 0.7955 (mmpt) cc_final: 0.7619 (mmmt) REVERT: B 19 ARG cc_start: 0.7465 (ttt-90) cc_final: 0.6449 (ttm110) REVERT: B 197 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7280 (mtp85) REVERT: B 258 ASP cc_start: 0.8529 (t0) cc_final: 0.8097 (t0) REVERT: E 51 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (tt) REVERT: E 113 GLN cc_start: 0.8270 (mm110) cc_final: 0.7898 (mm110) outliers start: 28 outliers final: 10 residues processed: 164 average time/residue: 0.5570 time to fit residues: 97.0095 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 chunk 19 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129337 restraints weight = 9971.147| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.93 r_work: 0.3204 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8958 Z= 0.094 Angle : 0.472 7.027 12145 Z= 0.253 Chirality : 0.041 0.164 1393 Planarity : 0.003 0.042 1528 Dihedral : 3.810 20.694 1239 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.98 % Allowed : 12.06 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.32 (0.25), residues: 1105 helix: 3.41 (0.25), residues: 389 sheet: 1.03 (0.30), residues: 281 loop : 0.17 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 32 TYR 0.007 0.001 TYR E 60 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8955) covalent geometry : angle 0.47158 (12139) SS BOND : bond 0.00309 ( 3) SS BOND : angle 0.59616 ( 6) hydrogen bonds : bond 0.03366 ( 451) hydrogen bonds : angle 4.24715 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.264 Fit side-chains REVERT: A 182 THR cc_start: 0.4772 (p) cc_final: 0.4538 (t) REVERT: A 312 LYS cc_start: 0.8023 (mmpt) cc_final: 0.7730 (mmmt) REVERT: A 318 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: B 19 ARG cc_start: 0.7533 (ttt-90) cc_final: 0.6521 (ttm110) REVERT: B 75 GLN cc_start: 0.8909 (mt0) cc_final: 0.8703 (mt0) REVERT: B 258 ASP cc_start: 0.8601 (t0) cc_final: 0.8350 (t0) REVERT: B 303 ASP cc_start: 0.8365 (m-30) cc_final: 0.8158 (m-30) REVERT: C 17 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: E 38 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8505 (ttm-80) REVERT: E 113 GLN cc_start: 0.8213 (mm110) cc_final: 0.7846 (mm110) REVERT: R 58 ARG cc_start: 0.6788 (tmt-80) cc_final: 0.5155 (mmt180) outliers start: 19 outliers final: 4 residues processed: 154 average time/residue: 0.5911 time to fit residues: 96.7026 Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 0.0070 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123242 restraints weight = 10110.845| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.02 r_work: 0.3130 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8958 Z= 0.171 Angle : 0.577 9.649 12145 Z= 0.303 Chirality : 0.044 0.178 1393 Planarity : 0.004 0.042 1528 Dihedral : 4.310 24.738 1239 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.43 % Allowed : 12.47 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.25), residues: 1105 helix: 3.06 (0.25), residues: 392 sheet: 0.82 (0.30), residues: 285 loop : -0.08 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 32 TYR 0.011 0.001 TYR R 383 PHE 0.017 0.002 PHE B 151 TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8955) covalent geometry : angle 0.57680 (12139) SS BOND : bond 0.00433 ( 3) SS BOND : angle 1.02032 ( 6) hydrogen bonds : bond 0.04357 ( 451) hydrogen bonds : angle 4.47097 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.327 Fit side-chains REVERT: A 9 ASP cc_start: 0.8142 (m-30) cc_final: 0.7929 (m-30) REVERT: A 273 LEU cc_start: 0.7513 (tt) cc_final: 0.6980 (mp) REVERT: A 312 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7685 (mmmt) REVERT: B 19 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.6587 (ttp80) REVERT: B 118 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8004 (p0) REVERT: B 197 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7429 (mtp85) REVERT: B 258 ASP cc_start: 0.8767 (t0) cc_final: 0.8423 (t0) REVERT: B 303 ASP cc_start: 0.8451 (m-30) cc_final: 0.8244 (m-30) REVERT: C 17 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: C 48 ASP cc_start: 0.8124 (t0) cc_final: 0.7916 (t0) REVERT: E 113 GLN cc_start: 0.8284 (mm110) cc_final: 0.7967 (mm110) REVERT: R 58 ARG cc_start: 0.6996 (tmt-80) cc_final: 0.5357 (mmt180) REVERT: R 139 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.5981 (tt0) REVERT: R 212 TYR cc_start: 0.7710 (t80) cc_final: 0.7501 (t80) REVERT: R 219 ARG cc_start: 0.6015 (tpm170) cc_final: 0.5727 (tpm170) outliers start: 33 outliers final: 12 residues processed: 147 average time/residue: 0.6056 time to fit residues: 94.5772 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124678 restraints weight = 9982.894| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.93 r_work: 0.3095 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8958 Z= 0.161 Angle : 0.563 9.086 12145 Z= 0.296 Chirality : 0.043 0.184 1393 Planarity : 0.004 0.045 1528 Dihedral : 4.326 25.325 1239 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.33 % Allowed : 13.93 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1105 helix: 2.99 (0.25), residues: 390 sheet: 0.89 (0.31), residues: 268 loop : -0.29 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 32 TYR 0.010 0.001 TYR R 383 PHE 0.017 0.001 PHE R 345 TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8955) covalent geometry : angle 0.56239 (12139) SS BOND : bond 0.00435 ( 3) SS BOND : angle 1.10495 ( 6) hydrogen bonds : bond 0.04234 ( 451) hydrogen bonds : angle 4.43499 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.340 Fit side-chains REVERT: A 9 ASP cc_start: 0.8208 (m-30) cc_final: 0.8004 (m-30) REVERT: A 273 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6812 (mp) REVERT: A 312 LYS cc_start: 0.7851 (mmpt) cc_final: 0.7570 (mmmt) REVERT: B 19 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.6501 (ttp80) REVERT: B 118 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7969 (p0) REVERT: B 258 ASP cc_start: 0.8722 (t0) cc_final: 0.8319 (t0) REVERT: B 260 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: B 262 MET cc_start: 0.8917 (ttm) cc_final: 0.8604 (ttm) REVERT: B 303 ASP cc_start: 0.8398 (m-30) cc_final: 0.8167 (m-30) REVERT: C 17 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: E 113 GLN cc_start: 0.8260 (mm110) cc_final: 0.7942 (mm110) REVERT: R 58 ARG cc_start: 0.6965 (tmt-80) cc_final: 0.5331 (mmt180) REVERT: R 139 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.5844 (tt0) REVERT: R 212 TYR cc_start: 0.7593 (t80) cc_final: 0.7361 (t80) REVERT: R 219 ARG cc_start: 0.5833 (tpm170) cc_final: 0.5553 (tpm170) REVERT: R 330 MET cc_start: 0.8014 (tpp) cc_final: 0.7811 (tpp) outliers start: 32 outliers final: 15 residues processed: 152 average time/residue: 0.5630 time to fit residues: 90.9758 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 7 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 186 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126978 restraints weight = 9973.014| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.93 r_work: 0.3127 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8958 Z= 0.108 Angle : 0.499 8.180 12145 Z= 0.265 Chirality : 0.041 0.147 1393 Planarity : 0.004 0.060 1528 Dihedral : 4.015 22.800 1239 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.70 % Allowed : 15.38 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1105 helix: 3.20 (0.26), residues: 388 sheet: 0.84 (0.31), residues: 273 loop : -0.22 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 32 TYR 0.007 0.001 TYR R 383 PHE 0.014 0.001 PHE R 345 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8955) covalent geometry : angle 0.49836 (12139) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.78590 ( 6) hydrogen bonds : bond 0.03568 ( 451) hydrogen bonds : angle 4.26394 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.289 Fit side-chains REVERT: A 273 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 312 LYS cc_start: 0.7977 (mmpt) cc_final: 0.7726 (mmmt) REVERT: B 19 ARG cc_start: 0.7372 (ttt-90) cc_final: 0.6448 (ttp80) REVERT: B 75 GLN cc_start: 0.9011 (mt0) cc_final: 0.8796 (mt0) REVERT: B 118 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7966 (p0) REVERT: B 258 ASP cc_start: 0.8696 (t0) cc_final: 0.8339 (t0) REVERT: B 260 GLU cc_start: 0.8482 (tt0) cc_final: 0.8184 (tt0) REVERT: B 262 MET cc_start: 0.8904 (ttm) cc_final: 0.8595 (ttm) REVERT: B 303 ASP cc_start: 0.8420 (m-30) cc_final: 0.8196 (m-30) REVERT: C 17 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: C 48 ASP cc_start: 0.8172 (t0) cc_final: 0.7952 (t0) REVERT: E 43 LYS cc_start: 0.8025 (mppt) cc_final: 0.7824 (mppt) REVERT: E 113 GLN cc_start: 0.8263 (mm110) cc_final: 0.7949 (mm110) REVERT: E 219 LEU cc_start: 0.7491 (tp) cc_final: 0.7263 (tp) REVERT: R 58 ARG cc_start: 0.6986 (tmt-80) cc_final: 0.5370 (mmt180) REVERT: R 61 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: R 139 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.5856 (tt0) REVERT: R 219 ARG cc_start: 0.5995 (tpm170) cc_final: 0.5750 (tpm170) REVERT: R 330 MET cc_start: 0.8048 (tpp) cc_final: 0.7612 (mmt) outliers start: 26 outliers final: 14 residues processed: 147 average time/residue: 0.5937 time to fit residues: 92.7051 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 186 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126523 restraints weight = 9942.584| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.93 r_work: 0.3131 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8958 Z= 0.114 Angle : 0.510 8.176 12145 Z= 0.269 Chirality : 0.041 0.158 1393 Planarity : 0.004 0.066 1528 Dihedral : 4.028 22.614 1239 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.43 % Allowed : 14.66 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.25), residues: 1105 helix: 3.15 (0.26), residues: 391 sheet: 0.88 (0.32), residues: 267 loop : -0.29 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 32 TYR 0.007 0.001 TYR R 383 PHE 0.014 0.001 PHE R 345 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8955) covalent geometry : angle 0.50960 (12139) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.86773 ( 6) hydrogen bonds : bond 0.03640 ( 451) hydrogen bonds : angle 4.24115 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.359 Fit side-chains REVERT: A 9 ASP cc_start: 0.8093 (m-30) cc_final: 0.7859 (m-30) REVERT: A 273 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6761 (mp) REVERT: A 312 LYS cc_start: 0.7985 (mmpt) cc_final: 0.7125 (mtpt) REVERT: B 19 ARG cc_start: 0.7386 (ttt-90) cc_final: 0.6394 (ttp80) REVERT: B 75 GLN cc_start: 0.9031 (mt0) cc_final: 0.8810 (mt0) REVERT: B 118 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8002 (p0) REVERT: B 258 ASP cc_start: 0.8695 (t0) cc_final: 0.8359 (t0) REVERT: B 262 MET cc_start: 0.8897 (ttm) cc_final: 0.8613 (ttm) REVERT: B 303 ASP cc_start: 0.8441 (m-30) cc_final: 0.8220 (m-30) REVERT: C 17 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: E 43 LYS cc_start: 0.8070 (mppt) cc_final: 0.7822 (mppt) REVERT: E 113 GLN cc_start: 0.8248 (mm110) cc_final: 0.7931 (mm110) REVERT: E 219 LEU cc_start: 0.7444 (tp) cc_final: 0.7217 (tp) REVERT: R 58 ARG cc_start: 0.6967 (tmt-80) cc_final: 0.5378 (mmt180) REVERT: R 61 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: R 219 ARG cc_start: 0.6037 (tpm170) cc_final: 0.5791 (tpm170) REVERT: R 330 MET cc_start: 0.8083 (tpp) cc_final: 0.7644 (mmt) outliers start: 33 outliers final: 19 residues processed: 152 average time/residue: 0.6074 time to fit residues: 97.8461 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 99 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127488 restraints weight = 9914.481| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.06 r_work: 0.3159 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8958 Z= 0.095 Angle : 0.477 7.327 12145 Z= 0.254 Chirality : 0.041 0.154 1393 Planarity : 0.004 0.073 1528 Dihedral : 3.852 20.658 1239 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.22 % Allowed : 14.97 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.26), residues: 1105 helix: 3.28 (0.26), residues: 389 sheet: 0.84 (0.31), residues: 271 loop : -0.22 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 32 TYR 0.007 0.001 TYR E 60 PHE 0.012 0.001 PHE R 345 TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8955) covalent geometry : angle 0.47702 (12139) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.69015 ( 6) hydrogen bonds : bond 0.03253 ( 451) hydrogen bonds : angle 4.11503 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.234 Fit side-chains REVERT: A 273 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 312 LYS cc_start: 0.7942 (mmpt) cc_final: 0.7116 (mtpt) REVERT: B 19 ARG cc_start: 0.7374 (ttt-90) cc_final: 0.6379 (ttp80) REVERT: B 38 ASP cc_start: 0.8005 (m-30) cc_final: 0.7802 (m-30) REVERT: B 75 GLN cc_start: 0.8993 (mt0) cc_final: 0.8787 (mt0) REVERT: B 118 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 258 ASP cc_start: 0.8670 (t0) cc_final: 0.8323 (t0) REVERT: B 262 MET cc_start: 0.8904 (ttm) cc_final: 0.8644 (ttm) REVERT: B 303 ASP cc_start: 0.8440 (m-30) cc_final: 0.8222 (m-30) REVERT: C 17 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: E 18 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8062 (tpp-160) REVERT: E 43 LYS cc_start: 0.8052 (mppt) cc_final: 0.7778 (mppt) REVERT: E 113 GLN cc_start: 0.8300 (mm110) cc_final: 0.7982 (mm110) REVERT: E 194 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8299 (m110) REVERT: E 219 LEU cc_start: 0.7425 (tp) cc_final: 0.7177 (tp) REVERT: R 58 ARG cc_start: 0.6933 (tmt-80) cc_final: 0.5293 (mmt180) REVERT: R 61 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: R 219 ARG cc_start: 0.6061 (tpm170) cc_final: 0.5821 (tpm170) REVERT: R 330 MET cc_start: 0.8029 (tpp) cc_final: 0.7665 (mmt) REVERT: R 348 THR cc_start: 0.8202 (m) cc_final: 0.7965 (p) outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 0.5614 time to fit residues: 93.2231 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125037 restraints weight = 9910.484| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.02 r_work: 0.3142 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8958 Z= 0.119 Angle : 0.516 8.825 12145 Z= 0.271 Chirality : 0.041 0.158 1393 Planarity : 0.004 0.076 1528 Dihedral : 4.002 21.924 1239 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.01 % Allowed : 15.70 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1105 helix: 3.20 (0.26), residues: 389 sheet: 0.92 (0.32), residues: 267 loop : -0.30 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 32 TYR 0.008 0.001 TYR R 383 PHE 0.013 0.001 PHE R 345 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8955) covalent geometry : angle 0.51526 (12139) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.96407 ( 6) hydrogen bonds : bond 0.03610 ( 451) hydrogen bonds : angle 4.19654 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.326 Fit side-chains REVERT: A 9 ASP cc_start: 0.8097 (m-30) cc_final: 0.7815 (m-30) REVERT: A 273 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6799 (mp) REVERT: A 312 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7738 (mmmt) REVERT: B 19 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.6407 (ttp80) REVERT: B 75 GLN cc_start: 0.9035 (mt0) cc_final: 0.8789 (mt0) REVERT: B 118 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7998 (p0) REVERT: B 262 MET cc_start: 0.8902 (ttm) cc_final: 0.8665 (ttm) REVERT: B 303 ASP cc_start: 0.8474 (m-30) cc_final: 0.8254 (m-30) REVERT: C 17 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: E 43 LYS cc_start: 0.8158 (mppt) cc_final: 0.7831 (mppt) REVERT: E 113 GLN cc_start: 0.8305 (mm110) cc_final: 0.7990 (mm110) REVERT: E 194 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8520 (m110) REVERT: E 219 LEU cc_start: 0.7415 (tp) cc_final: 0.7140 (tp) REVERT: R 58 ARG cc_start: 0.6982 (tmt-80) cc_final: 0.5346 (mmt180) REVERT: R 61 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: R 219 ARG cc_start: 0.6058 (tpm170) cc_final: 0.5819 (tpm170) REVERT: R 330 MET cc_start: 0.8116 (tpp) cc_final: 0.7684 (mmt) REVERT: R 348 THR cc_start: 0.8186 (m) cc_final: 0.7930 (p) outliers start: 29 outliers final: 20 residues processed: 148 average time/residue: 0.5709 time to fit residues: 90.0909 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.170009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124613 restraints weight = 9898.725| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.97 r_work: 0.3135 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8958 Z= 0.132 Angle : 0.531 8.830 12145 Z= 0.280 Chirality : 0.042 0.162 1393 Planarity : 0.004 0.078 1528 Dihedral : 4.093 22.688 1239 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.12 % Allowed : 15.70 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1105 helix: 3.11 (0.26), residues: 392 sheet: 0.88 (0.32), residues: 267 loop : -0.36 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 32 TYR 0.008 0.001 TYR R 383 PHE 0.014 0.001 PHE R 345 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8955) covalent geometry : angle 0.53090 (12139) SS BOND : bond 0.00349 ( 3) SS BOND : angle 1.07653 ( 6) hydrogen bonds : bond 0.03767 ( 451) hydrogen bonds : angle 4.25425 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.338 Fit side-chains REVERT: A 9 ASP cc_start: 0.8094 (m-30) cc_final: 0.7816 (m-30) REVERT: A 273 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6783 (mp) REVERT: A 312 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7688 (mmmt) REVERT: B 19 ARG cc_start: 0.7394 (ttt-90) cc_final: 0.6398 (ttp80) REVERT: B 75 GLN cc_start: 0.9033 (mt0) cc_final: 0.8809 (mt0) REVERT: B 118 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7974 (p0) REVERT: B 258 ASP cc_start: 0.8660 (t0) cc_final: 0.8278 (t0) REVERT: B 262 MET cc_start: 0.8883 (ttm) cc_final: 0.8663 (ttm) REVERT: B 303 ASP cc_start: 0.8459 (m-30) cc_final: 0.8237 (m-30) REVERT: C 17 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: E 43 LYS cc_start: 0.8145 (mppt) cc_final: 0.7776 (mppt) REVERT: E 113 GLN cc_start: 0.8241 (mm110) cc_final: 0.7918 (mm110) REVERT: E 219 LEU cc_start: 0.7510 (tp) cc_final: 0.7254 (tp) REVERT: R 58 ARG cc_start: 0.6963 (tmt-80) cc_final: 0.5403 (mmt180) REVERT: R 61 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: R 219 ARG cc_start: 0.6048 (tpm170) cc_final: 0.5809 (tpm170) REVERT: R 330 MET cc_start: 0.8107 (tpp) cc_final: 0.7661 (mmt) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.5581 time to fit residues: 88.5904 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 186 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.172730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126004 restraints weight = 9807.779| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.92 r_work: 0.3150 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8958 Z= 0.122 Angle : 0.518 8.070 12145 Z= 0.273 Chirality : 0.042 0.161 1393 Planarity : 0.004 0.079 1528 Dihedral : 4.060 22.422 1239 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.70 % Allowed : 16.11 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.25), residues: 1105 helix: 3.12 (0.26), residues: 392 sheet: 0.88 (0.32), residues: 267 loop : -0.38 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 32 TYR 0.008 0.001 TYR R 383 PHE 0.014 0.001 PHE R 345 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8955) covalent geometry : angle 0.51725 (12139) SS BOND : bond 0.00317 ( 3) SS BOND : angle 1.08949 ( 6) hydrogen bonds : bond 0.03684 ( 451) hydrogen bonds : angle 4.24903 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.08 seconds wall clock time: 70 minutes 38.58 seconds (4238.58 seconds total)