Starting phenix.real_space_refine on Fri Jan 17 06:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xos_38539/01_2025/8xos_38539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xos_38539/01_2025/8xos_38539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xos_38539/01_2025/8xos_38539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xos_38539/01_2025/8xos_38539.map" model { file = "/net/cci-nas-00/data/ceres_data/8xos_38539/01_2025/8xos_38539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xos_38539/01_2025/8xos_38539.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1946 atoms to isotropic. 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 65 5.16 5 C 5713 2.51 5 N 1476 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8919 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2577 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} 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: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2335 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.47, per 1000 atoms: 0.61 Number of scatterers: 8919 At special positions: 0 Unit cell: (116.739, 94.248, 117.81, 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 65 16.00 O 1665 8.00 N 1476 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 175 " - pdb=" SG CYS R 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.511A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 207 through 218 removed outlier: 4.707A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.434A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.504A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 89 through 98 Processing helix chain 'R' and resid 103 through 127 Proline residue: R 118 - end of helix Processing helix chain 'R' and resid 135 through 154 removed outlier: 3.553A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 164 removed outlier: 3.872A pdb=" N LYS R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 206 Processing helix chain 'R' and resid 206 through 214 removed outlier: 3.618A pdb=" N LEU R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 234 removed outlier: 3.653A pdb=" N VAL R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 240 Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 298 Processing helix chain 'R' and resid 308 through 325 Processing helix chain 'R' and resid 326 through 337 Processing helix chain 'R' and resid 342 through 361 removed outlier: 4.407A pdb=" N GLU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Proline residue: R 368 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.071A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.531A 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: 3.578A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.916A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.543A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.843A 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: 6.427A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.686A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.772A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.573A 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: 6.513A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.513A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.152A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 87 through 88 446 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2817 1.34 - 1.46: 2032 1.46 - 1.58: 4174 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9114 Sorted by residual: bond pdb=" CD2 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.374 1.397 -0.023 1.10e-02 8.26e+03 4.40e+00 bond pdb=" N SER A 6 " pdb=" CA SER A 6 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.62e+00 bond pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " ideal model delta sigma weight residual 1.550 1.513 0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.550 1.514 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CE1 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.321 1.339 -0.018 1.00e-02 1.00e+04 3.22e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 11435 1.58 - 3.16: 786 3.16 - 4.73: 111 4.73 - 6.31: 18 6.31 - 7.89: 10 Bond angle restraints: 12360 Sorted by residual: angle pdb=" CB HIS E 35 " pdb=" CG HIS E 35 " pdb=" CD2 HIS E 35 " ideal model delta sigma weight residual 131.20 125.42 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CB HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 131.20 125.62 5.58 1.30e+00 5.92e-01 1.84e+01 angle pdb=" CB HIS E 232 " pdb=" CG HIS E 232 " pdb=" CD2 HIS E 232 " ideal model delta sigma weight residual 131.20 126.66 4.54 1.30e+00 5.92e-01 1.22e+01 angle pdb=" ND1 HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 106.10 109.54 -3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CB ARG B 314 " pdb=" CG ARG B 314 " pdb=" CD ARG B 314 " ideal model delta sigma weight residual 111.30 103.41 7.89 2.30e+00 1.89e-01 1.18e+01 ... (remaining 12355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5080 17.74 - 35.49: 324 35.49 - 53.23: 55 53.23 - 70.97: 18 70.97 - 88.72: 5 Dihedral angle restraints: 5482 sinusoidal: 2174 harmonic: 3308 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ALA E 92 " pdb=" C ALA E 92 " pdb=" N MET E 93 " pdb=" CA MET E 93 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1129 0.068 - 0.135: 257 0.135 - 0.202: 24 0.202 - 0.270: 3 0.270 - 0.337: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" C13 CLR R 601 " pdb=" C12 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C17 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1412 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 59 " -0.081 2.00e-02 2.50e+03 4.15e-02 3.44e+01 pdb=" CG TYR E 59 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 59 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 59 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 59 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 59 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 101 " 0.059 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" CG TYR E 101 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 101 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 101 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR E 101 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR E 101 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 101 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 101 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 191 " -0.090 9.50e-02 1.11e+02 5.24e-02 1.50e+01 pdb=" NE ARG E 191 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG E 191 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG E 191 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG E 191 " 0.018 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 970 2.74 - 3.28: 9488 3.28 - 3.82: 14879 3.82 - 4.36: 18335 4.36 - 4.90: 31266 Nonbonded interactions: 74938 Sorted by model distance: nonbonded pdb=" CE1 PHE B 253 " pdb=" CG GLU B 260 " model vdw 2.197 3.740 nonbonded pdb=" CD2 TYR E 50 " pdb=" OH TYR E 235 " model vdw 2.236 3.340 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OG SER A 281 " model vdw 2.255 3.040 nonbonded pdb=" O GLY R 165 " pdb=" OG SER R 166 " model vdw 2.289 3.040 ... (remaining 74933 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.008 0.060 9114 Z= 0.527 Angle : 0.900 7.888 12360 Z= 0.523 Chirality : 0.057 0.337 1415 Planarity : 0.007 0.052 1540 Dihedral : 12.894 88.719 3345 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.72 % Allowed : 4.42 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1116 helix: -0.52 (0.25), residues: 377 sheet: 0.32 (0.30), residues: 269 loop : -0.91 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP E 47 HIS 0.011 0.002 HIS R 143 PHE 0.040 0.003 PHE E 177 TYR 0.081 0.007 TYR E 59 ARG 0.065 0.009 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t0) REVERT: A 204 GLN cc_start: 0.9165 (pp30) cc_final: 0.8878 (pp30) REVERT: B 12 GLU cc_start: 0.9425 (tp30) cc_final: 0.9176 (tp30) REVERT: B 17 GLN cc_start: 0.9594 (tm-30) cc_final: 0.9271 (tm-30) REVERT: B 32 GLN cc_start: 0.8902 (mt0) cc_final: 0.8662 (mt0) REVERT: B 220 GLN cc_start: 0.9068 (mt0) cc_final: 0.8776 (mt0) REVERT: C 58 GLU cc_start: 0.8248 (tp30) cc_final: 0.8010 (tp30) REVERT: E 73 ASP cc_start: 0.8323 (t0) cc_final: 0.8009 (t70) REVERT: E 120 SER cc_start: 0.8709 (t) cc_final: 0.8503 (p) REVERT: E 230 MET cc_start: 0.9003 (tmm) cc_final: 0.8432 (ttt) REVERT: R 167 ASP cc_start: 0.8660 (t0) cc_final: 0.8457 (t70) REVERT: R 193 MET cc_start: 0.8832 (mtm) cc_final: 0.8614 (mtt) REVERT: R 347 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8106 (mm-30) REVERT: R 367 ASP cc_start: 0.8635 (m-30) cc_final: 0.8434 (m-30) outliers start: 7 outliers final: 3 residues processed: 206 average time/residue: 0.2997 time to fit residues: 78.9678 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain R residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 62 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN B 295 ASN B 340 ASN C 24 ASN R 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059958 restraints weight = 21623.138| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.31 r_work: 0.2770 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9114 Z= 0.216 Angle : 0.647 7.162 12360 Z= 0.345 Chirality : 0.044 0.207 1415 Planarity : 0.005 0.050 1540 Dihedral : 6.910 54.350 1359 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.36 % Allowed : 9.15 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1116 helix: 1.21 (0.26), residues: 370 sheet: 0.30 (0.29), residues: 284 loop : -0.37 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS R 143 PHE 0.022 0.001 PHE A 196 TYR 0.029 0.002 TYR E 235 ARG 0.006 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8737 (t70) cc_final: 0.8440 (t0) REVERT: A 204 GLN cc_start: 0.9270 (pp30) cc_final: 0.8660 (pp30) REVERT: A 243 MET cc_start: 0.8597 (tpp) cc_final: 0.7372 (tpp) REVERT: B 10 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8918 (mp0) REVERT: B 215 GLU cc_start: 0.9150 (mp0) cc_final: 0.8578 (mp0) REVERT: C 58 GLU cc_start: 0.8723 (tp30) cc_final: 0.8386 (tp30) REVERT: E 62 ASP cc_start: 0.9102 (m-30) cc_final: 0.8890 (p0) REVERT: E 93 MET cc_start: 0.8759 (tpp) cc_final: 0.8557 (tpp) REVERT: E 120 SER cc_start: 0.8641 (t) cc_final: 0.8394 (p) REVERT: E 220 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8492 (mp0) REVERT: E 223 ASP cc_start: 0.9204 (m-30) cc_final: 0.8795 (m-30) REVERT: E 244 LYS cc_start: 0.9235 (tttt) cc_final: 0.8919 (tptp) REVERT: E 246 GLU cc_start: 0.7297 (pm20) cc_final: 0.7058 (pm20) REVERT: R 167 ASP cc_start: 0.8754 (t0) cc_final: 0.8476 (t70) REVERT: R 347 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8310 (mm-30) outliers start: 23 outliers final: 9 residues processed: 153 average time/residue: 0.2439 time to fit residues: 50.4016 Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 9.9990 chunk 86 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061932 restraints weight = 21622.944| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.35 r_work: 0.2799 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9114 Z= 0.173 Angle : 0.587 7.037 12360 Z= 0.310 Chirality : 0.042 0.179 1415 Planarity : 0.004 0.051 1540 Dihedral : 5.750 49.828 1356 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.34 % Allowed : 11.51 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1116 helix: 1.44 (0.27), residues: 377 sheet: 0.57 (0.30), residues: 278 loop : -0.28 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS R 336 PHE 0.026 0.001 PHE E 68 TYR 0.019 0.001 TYR E 235 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8736 (t70) cc_final: 0.8456 (t0) REVERT: A 204 GLN cc_start: 0.9200 (pp30) cc_final: 0.8629 (pp30) REVERT: A 243 MET cc_start: 0.8438 (tpp) cc_final: 0.7518 (tpp) REVERT: B 12 GLU cc_start: 0.9269 (tp30) cc_final: 0.8905 (tp30) REVERT: B 13 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8935 (mm-40) REVERT: C 17 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9313 (tm-30) REVERT: C 20 LYS cc_start: 0.9422 (pptt) cc_final: 0.9165 (pptt) REVERT: C 22 GLU cc_start: 0.8013 (tp30) cc_final: 0.7797 (tt0) REVERT: C 30 VAL cc_start: 0.8529 (t) cc_final: 0.8183 (p) REVERT: C 58 GLU cc_start: 0.8665 (tp30) cc_final: 0.8308 (tp30) REVERT: E 46 GLU cc_start: 0.8800 (pt0) cc_final: 0.8594 (pt0) REVERT: E 62 ASP cc_start: 0.9062 (m-30) cc_final: 0.8796 (p0) REVERT: E 73 ASP cc_start: 0.7976 (t0) cc_final: 0.7557 (t70) REVERT: E 93 MET cc_start: 0.8778 (tpp) cc_final: 0.8559 (tpp) REVERT: E 120 SER cc_start: 0.8690 (t) cc_final: 0.8483 (p) REVERT: E 220 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8468 (mp0) REVERT: E 223 ASP cc_start: 0.9193 (m-30) cc_final: 0.8445 (m-30) REVERT: E 230 MET cc_start: 0.8932 (tmm) cc_final: 0.8667 (ttm) REVERT: R 134 LYS cc_start: 0.8617 (pttt) cc_final: 0.8319 (ptmm) REVERT: R 167 ASP cc_start: 0.8630 (t0) cc_final: 0.8342 (t70) REVERT: R 347 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8231 (mm-30) outliers start: 13 outliers final: 9 residues processed: 156 average time/residue: 0.2410 time to fit residues: 51.0538 Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060739 restraints weight = 21427.280| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.32 r_work: 0.2787 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9114 Z= 0.190 Angle : 0.579 7.276 12360 Z= 0.303 Chirality : 0.042 0.247 1415 Planarity : 0.004 0.056 1540 Dihedral : 5.430 49.121 1356 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.36 % Allowed : 11.92 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1116 helix: 1.55 (0.27), residues: 377 sheet: 0.63 (0.31), residues: 279 loop : -0.23 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.029 0.001 PHE E 68 TYR 0.023 0.001 TYR E 235 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8748 (t70) cc_final: 0.8450 (t0) REVERT: A 204 GLN cc_start: 0.9184 (pp30) cc_final: 0.8557 (pp30) REVERT: A 261 ASP cc_start: 0.9275 (p0) cc_final: 0.9046 (p0) REVERT: B 32 GLN cc_start: 0.8864 (mt0) cc_final: 0.8636 (mt0) REVERT: B 307 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8979 (t) REVERT: C 17 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9190 (tm-30) REVERT: C 22 GLU cc_start: 0.7970 (tp30) cc_final: 0.7642 (tt0) REVERT: C 30 VAL cc_start: 0.8506 (t) cc_final: 0.8189 (p) REVERT: C 58 GLU cc_start: 0.8740 (tp30) cc_final: 0.8369 (tp30) REVERT: E 62 ASP cc_start: 0.9159 (m-30) cc_final: 0.8812 (p0) REVERT: E 73 ASP cc_start: 0.8015 (t0) cc_final: 0.7659 (t70) REVERT: E 120 SER cc_start: 0.8697 (t) cc_final: 0.8477 (p) REVERT: E 183 GLN cc_start: 0.8877 (mt0) cc_final: 0.8641 (pt0) REVERT: E 223 ASP cc_start: 0.9124 (m-30) cc_final: 0.8194 (m-30) REVERT: E 230 MET cc_start: 0.8887 (tmm) cc_final: 0.8664 (ttm) REVERT: R 158 LYS cc_start: 0.9371 (mttm) cc_final: 0.9157 (mttt) REVERT: R 167 ASP cc_start: 0.8630 (t0) cc_final: 0.8365 (t70) REVERT: R 347 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8210 (mm-30) outliers start: 23 outliers final: 13 residues processed: 151 average time/residue: 0.2229 time to fit residues: 47.0368 Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 19 optimal weight: 0.0770 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057239 restraints weight = 21602.505| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.33 r_work: 0.2704 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9114 Z= 0.361 Angle : 0.649 8.912 12360 Z= 0.340 Chirality : 0.045 0.286 1415 Planarity : 0.004 0.058 1540 Dihedral : 5.687 53.180 1356 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.98 % Allowed : 12.64 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1116 helix: 1.47 (0.27), residues: 377 sheet: 0.52 (0.31), residues: 281 loop : -0.34 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 100 HIS 0.006 0.001 HIS B 225 PHE 0.024 0.002 PHE E 68 TYR 0.028 0.002 TYR E 235 ARG 0.005 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8874 (t70) cc_final: 0.8511 (t0) REVERT: A 22 ASN cc_start: 0.9098 (m-40) cc_final: 0.8868 (t0) REVERT: A 204 GLN cc_start: 0.9191 (pp30) cc_final: 0.8598 (pp30) REVERT: B 10 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8681 (mp0) REVERT: B 307 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8865 (t) REVERT: C 17 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9312 (tm-30) REVERT: C 58 GLU cc_start: 0.8808 (tp30) cc_final: 0.8407 (tp30) REVERT: E 46 GLU cc_start: 0.8857 (pt0) cc_final: 0.8470 (pt0) REVERT: E 62 ASP cc_start: 0.9219 (m-30) cc_final: 0.8913 (p0) REVERT: E 73 ASP cc_start: 0.8053 (t0) cc_final: 0.7704 (t70) REVERT: E 120 SER cc_start: 0.8705 (t) cc_final: 0.8481 (p) REVERT: E 183 GLN cc_start: 0.8924 (mt0) cc_final: 0.8691 (pt0) REVERT: E 223 ASP cc_start: 0.9085 (m-30) cc_final: 0.8743 (m-30) REVERT: E 230 MET cc_start: 0.8919 (tmm) cc_final: 0.8603 (ttt) REVERT: R 134 LYS cc_start: 0.8639 (pttp) cc_final: 0.8372 (ptmm) REVERT: R 167 ASP cc_start: 0.8615 (t0) cc_final: 0.8359 (t70) REVERT: R 347 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8209 (mm-30) REVERT: R 367 ASP cc_start: 0.8948 (m-30) cc_final: 0.8731 (m-30) outliers start: 29 outliers final: 18 residues processed: 143 average time/residue: 0.2258 time to fit residues: 44.3972 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059056 restraints weight = 21357.566| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.31 r_work: 0.2748 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9114 Z= 0.217 Angle : 0.602 10.805 12360 Z= 0.314 Chirality : 0.043 0.342 1415 Planarity : 0.004 0.055 1540 Dihedral : 5.379 50.835 1356 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.16 % Allowed : 14.08 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1116 helix: 1.46 (0.27), residues: 378 sheet: 0.51 (0.31), residues: 279 loop : -0.31 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.028 0.001 PHE E 68 TYR 0.023 0.001 TYR E 235 ARG 0.002 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8797 (t70) cc_final: 0.8460 (t0) REVERT: A 22 ASN cc_start: 0.9048 (m-40) cc_final: 0.8821 (t0) REVERT: A 287 TYR cc_start: 0.8815 (m-80) cc_final: 0.8471 (m-80) REVERT: B 32 GLN cc_start: 0.8963 (mt0) cc_final: 0.8677 (mt0) REVERT: B 259 GLN cc_start: 0.7936 (tt0) cc_final: 0.7452 (mt0) REVERT: B 307 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8898 (t) REVERT: C 58 GLU cc_start: 0.8842 (tp30) cc_final: 0.8442 (tp30) REVERT: E 46 GLU cc_start: 0.8819 (pt0) cc_final: 0.8423 (pt0) REVERT: E 62 ASP cc_start: 0.9185 (m-30) cc_final: 0.8834 (p0) REVERT: E 73 ASP cc_start: 0.8039 (t0) cc_final: 0.7633 (t70) REVERT: E 120 SER cc_start: 0.8687 (t) cc_final: 0.8476 (p) REVERT: E 183 GLN cc_start: 0.8904 (mt0) cc_final: 0.8686 (pt0) REVERT: E 223 ASP cc_start: 0.9042 (m-30) cc_final: 0.8710 (m-30) REVERT: E 230 MET cc_start: 0.8899 (tmm) cc_final: 0.8528 (ttt) REVERT: R 101 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9177 (mp) REVERT: R 141 MET cc_start: 0.9144 (mmm) cc_final: 0.8712 (mmm) REVERT: R 167 ASP cc_start: 0.8484 (t0) cc_final: 0.8223 (t70) REVERT: R 258 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8107 (mp) REVERT: R 347 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8176 (mm-30) REVERT: R 367 ASP cc_start: 0.8881 (m-30) cc_final: 0.8668 (m-30) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.2260 time to fit residues: 45.0493 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 199 ASP Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059870 restraints weight = 21539.237| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.34 r_work: 0.2768 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9114 Z= 0.192 Angle : 0.593 11.467 12360 Z= 0.307 Chirality : 0.042 0.315 1415 Planarity : 0.004 0.056 1540 Dihedral : 5.144 48.645 1356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 14.90 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1116 helix: 1.54 (0.27), residues: 379 sheet: 0.46 (0.31), residues: 280 loop : -0.35 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.001 PHE E 68 TYR 0.021 0.001 TYR E 235 ARG 0.003 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8803 (t70) cc_final: 0.8485 (t0) REVERT: A 22 ASN cc_start: 0.9070 (m-40) cc_final: 0.8855 (t0) REVERT: A 32 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.8327 (ttm-80) REVERT: A 53 MET cc_start: 0.9152 (mpp) cc_final: 0.8932 (mpp) REVERT: A 256 ASN cc_start: 0.8485 (t0) cc_final: 0.8092 (t0) REVERT: A 287 TYR cc_start: 0.8764 (m-80) cc_final: 0.8509 (m-80) REVERT: B 32 GLN cc_start: 0.9023 (mt0) cc_final: 0.8804 (mt0) REVERT: B 259 GLN cc_start: 0.7989 (tt0) cc_final: 0.7478 (mt0) REVERT: B 307 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8950 (t) REVERT: C 58 GLU cc_start: 0.8805 (tp30) cc_final: 0.8414 (tp30) REVERT: E 46 GLU cc_start: 0.8781 (pt0) cc_final: 0.8394 (pt0) REVERT: E 62 ASP cc_start: 0.9129 (m-30) cc_final: 0.8794 (p0) REVERT: E 73 ASP cc_start: 0.8185 (t0) cc_final: 0.7744 (t70) REVERT: E 120 SER cc_start: 0.8732 (t) cc_final: 0.8463 (p) REVERT: E 153 GLU cc_start: 0.8739 (pt0) cc_final: 0.8318 (pm20) REVERT: E 223 ASP cc_start: 0.9034 (m-30) cc_final: 0.8713 (m-30) REVERT: E 230 MET cc_start: 0.8869 (tmm) cc_final: 0.8522 (ttt) REVERT: R 141 MET cc_start: 0.9130 (mmm) cc_final: 0.8704 (mmm) REVERT: R 347 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8340 (mm-30) REVERT: R 367 ASP cc_start: 0.8840 (m-30) cc_final: 0.8612 (m-30) outliers start: 18 outliers final: 14 residues processed: 142 average time/residue: 0.2242 time to fit residues: 43.5546 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.084887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060980 restraints weight = 21665.193| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.33 r_work: 0.2792 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.165 Angle : 0.588 10.043 12360 Z= 0.304 Chirality : 0.042 0.305 1415 Planarity : 0.003 0.056 1540 Dihedral : 4.986 48.010 1356 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.36 % Allowed : 15.01 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1116 helix: 1.61 (0.27), residues: 379 sheet: 0.51 (0.31), residues: 281 loop : -0.29 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.000 HIS B 225 PHE 0.014 0.001 PHE A 196 TYR 0.021 0.001 TYR E 235 ARG 0.003 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8773 (t70) cc_final: 0.8464 (t0) REVERT: A 32 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8220 (ttm-80) REVERT: A 256 ASN cc_start: 0.8456 (t0) cc_final: 0.8080 (t0) REVERT: A 287 TYR cc_start: 0.8744 (m-80) cc_final: 0.8536 (m-80) REVERT: B 10 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8826 (mp0) REVERT: B 32 GLN cc_start: 0.9029 (mt0) cc_final: 0.8793 (mt0) REVERT: B 259 GLN cc_start: 0.8032 (tt0) cc_final: 0.7536 (mt0) REVERT: B 307 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8950 (t) REVERT: C 58 GLU cc_start: 0.8827 (tp30) cc_final: 0.8451 (tp30) REVERT: E 46 GLU cc_start: 0.8782 (pt0) cc_final: 0.8375 (pt0) REVERT: E 62 ASP cc_start: 0.9139 (m-30) cc_final: 0.8826 (p0) REVERT: E 73 ASP cc_start: 0.8271 (t0) cc_final: 0.7893 (t70) REVERT: E 93 MET cc_start: 0.8876 (tpp) cc_final: 0.8609 (tpp) REVERT: E 120 SER cc_start: 0.8753 (t) cc_final: 0.8494 (p) REVERT: E 153 GLU cc_start: 0.8737 (pt0) cc_final: 0.8288 (pm20) REVERT: E 223 ASP cc_start: 0.9045 (m-30) cc_final: 0.8711 (m-30) REVERT: E 230 MET cc_start: 0.8850 (tmm) cc_final: 0.8622 (ttt) REVERT: R 101 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9138 (mp) REVERT: R 141 MET cc_start: 0.9124 (mmm) cc_final: 0.8710 (mmm) REVERT: R 148 ASP cc_start: 0.8810 (m-30) cc_final: 0.8589 (t0) REVERT: R 167 ASP cc_start: 0.8363 (t0) cc_final: 0.7966 (t70) REVERT: R 347 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8322 (mm-30) outliers start: 23 outliers final: 14 residues processed: 149 average time/residue: 0.2334 time to fit residues: 47.5524 Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 132 LYS Chi-restraints excluded: chain R residue 199 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.083514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059328 restraints weight = 21629.390| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.33 r_work: 0.2759 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9114 Z= 0.233 Angle : 0.619 9.008 12360 Z= 0.319 Chirality : 0.043 0.280 1415 Planarity : 0.004 0.053 1540 Dihedral : 5.138 49.759 1356 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.06 % Allowed : 15.31 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1116 helix: 1.56 (0.27), residues: 385 sheet: 0.49 (0.31), residues: 281 loop : -0.39 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.030 0.001 PHE E 68 TYR 0.024 0.001 TYR E 235 ARG 0.003 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8798 (t70) cc_final: 0.8453 (t0) REVERT: A 32 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.8302 (ttm-80) REVERT: A 53 MET cc_start: 0.9168 (mpp) cc_final: 0.8947 (mpp) REVERT: A 256 ASN cc_start: 0.8458 (t0) cc_final: 0.8059 (t0) REVERT: A 287 TYR cc_start: 0.8759 (m-80) cc_final: 0.8554 (m-80) REVERT: B 32 GLN cc_start: 0.9097 (mt0) cc_final: 0.8823 (mt0) REVERT: B 259 GLN cc_start: 0.8051 (tt0) cc_final: 0.7557 (mt0) REVERT: B 307 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8936 (t) REVERT: C 36 ASP cc_start: 0.8936 (t0) cc_final: 0.8671 (t0) REVERT: C 58 GLU cc_start: 0.8860 (tp30) cc_final: 0.8473 (tp30) REVERT: E 46 GLU cc_start: 0.8776 (pt0) cc_final: 0.8366 (pt0) REVERT: E 62 ASP cc_start: 0.9144 (m-30) cc_final: 0.8844 (p0) REVERT: E 73 ASP cc_start: 0.8253 (t0) cc_final: 0.7840 (t70) REVERT: E 93 MET cc_start: 0.8866 (tpp) cc_final: 0.8598 (tpp) REVERT: E 120 SER cc_start: 0.8719 (t) cc_final: 0.8480 (p) REVERT: E 223 ASP cc_start: 0.9007 (m-30) cc_final: 0.8461 (m-30) REVERT: E 230 MET cc_start: 0.8881 (tmm) cc_final: 0.8566 (ttt) REVERT: R 101 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9145 (mp) REVERT: R 141 MET cc_start: 0.9108 (mmm) cc_final: 0.8699 (mmm) REVERT: R 148 ASP cc_start: 0.8958 (m-30) cc_final: 0.8683 (t70) REVERT: R 167 ASP cc_start: 0.8405 (t0) cc_final: 0.8010 (t70) REVERT: R 258 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8261 (mp) REVERT: R 347 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8335 (mm-30) outliers start: 20 outliers final: 16 residues processed: 140 average time/residue: 0.2438 time to fit residues: 46.1116 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 132 LYS Chi-restraints excluded: chain R residue 199 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.081155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056860 restraints weight = 21788.281| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.33 r_work: 0.2696 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9114 Z= 0.389 Angle : 0.698 12.366 12360 Z= 0.360 Chirality : 0.046 0.340 1415 Planarity : 0.004 0.056 1540 Dihedral : 5.593 52.648 1356 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.95 % Allowed : 15.42 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1116 helix: 1.44 (0.27), residues: 385 sheet: 0.33 (0.31), residues: 289 loop : -0.52 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 100 HIS 0.005 0.001 HIS B 225 PHE 0.018 0.002 PHE E 68 TYR 0.028 0.002 TYR E 235 ARG 0.005 0.000 ARG R 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8884 (t70) cc_final: 0.8487 (t0) REVERT: A 287 TYR cc_start: 0.8850 (m-80) cc_final: 0.8586 (m-80) REVERT: B 32 GLN cc_start: 0.9144 (mt0) cc_final: 0.8907 (mt0) REVERT: B 259 GLN cc_start: 0.8125 (tt0) cc_final: 0.7685 (mt0) REVERT: B 307 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8892 (t) REVERT: C 20 LYS cc_start: 0.9479 (pptt) cc_final: 0.9181 (pptt) REVERT: C 36 ASP cc_start: 0.8964 (t0) cc_final: 0.8692 (t0) REVERT: C 58 GLU cc_start: 0.8883 (tp30) cc_final: 0.8467 (tp30) REVERT: E 46 GLU cc_start: 0.8831 (pt0) cc_final: 0.8390 (pt0) REVERT: E 62 ASP cc_start: 0.9179 (m-30) cc_final: 0.8942 (p0) REVERT: E 73 ASP cc_start: 0.8281 (t0) cc_final: 0.7850 (t70) REVERT: E 93 MET cc_start: 0.8886 (tpp) cc_final: 0.8627 (tpp) REVERT: E 120 SER cc_start: 0.8778 (t) cc_final: 0.8499 (p) REVERT: E 223 ASP cc_start: 0.8704 (m-30) cc_final: 0.8450 (m-30) REVERT: E 230 MET cc_start: 0.8923 (tmm) cc_final: 0.8635 (ttt) REVERT: R 141 MET cc_start: 0.9140 (mmm) cc_final: 0.8708 (mmm) REVERT: R 148 ASP cc_start: 0.9014 (m-30) cc_final: 0.8720 (t70) REVERT: R 167 ASP cc_start: 0.8492 (t0) cc_final: 0.8111 (t70) REVERT: R 240 LYS cc_start: 0.7736 (mmmm) cc_final: 0.7418 (mmtm) REVERT: R 258 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8527 (mp) REVERT: R 347 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8373 (mm-30) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.2388 time to fit residues: 42.7690 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 132 LYS Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.084564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060606 restraints weight = 21359.435| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.32 r_work: 0.2786 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9114 Z= 0.177 Angle : 0.628 12.733 12360 Z= 0.320 Chirality : 0.043 0.340 1415 Planarity : 0.003 0.052 1540 Dihedral : 5.190 49.897 1356 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.64 % Allowed : 15.62 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1116 helix: 1.57 (0.27), residues: 379 sheet: 0.39 (0.31), residues: 281 loop : -0.32 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE A 196 TYR 0.019 0.001 TYR E 235 ARG 0.003 0.000 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.88 seconds wall clock time: 78 minutes 36.02 seconds (4716.02 seconds total)