Starting phenix.real_space_refine on Wed Sep 17 13:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpe_62485/09_2025/9kpe_62485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpe_62485/09_2025/9kpe_62485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kpe_62485/09_2025/9kpe_62485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpe_62485/09_2025/9kpe_62485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kpe_62485/09_2025/9kpe_62485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpe_62485/09_2025/9kpe_62485.map" } resolution = 3.35 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= 0.001 sd= 0.022 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 65 5.16 5 C 5697 2.51 5 N 1498 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1814 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2247 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.29, per 1000 atoms: 0.26 Number of scatterers: 8916 At special positions: 0 Unit cell: (88.4, 121.68, 118.56, 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 1656 8.00 N 1498 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 69 " - pdb=" SG CYS R 79 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 347.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 38.9% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.684A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.707A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.097A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.738A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.697A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.423A 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 270 through 278 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.710A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.597A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.561A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.544A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.644A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 39 Processing helix chain 'R' and resid 43 through 72 removed outlier: 3.584A pdb=" N MET R 47 " --> pdb=" O MET R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 108 removed outlier: 3.650A pdb=" N SER R 108 " --> pdb=" O CYS R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 125 Processing helix chain 'R' and resid 125 through 156 Proline residue: R 143 - end of helix Processing helix chain 'R' and resid 172 through 208 Proline residue: R 188 - end of helix Processing helix chain 'R' and resid 217 through 249 Processing helix chain 'R' and resid 257 through 279 removed outlier: 3.590A pdb=" N TRP R 261 " --> pdb=" O TRP R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 287 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.154A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.801A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.494A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.272A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.613A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.183A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.092A 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 151 removed outlier: 3.757A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.440A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.722A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.739A 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 276 removed outlier: 6.620A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 297 removed outlier: 4.005A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.063A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 17 through 23 Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.151A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1269 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: 1.48 Time building geometry restraints manager: 1.19 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: 2842 1.34 - 1.46: 2282 1.46 - 1.58: 3890 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9109 Sorted by residual: bond pdb=" CA ASP B 205 " pdb=" C ASP B 205 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.80e-02 3.09e+03 2.96e+00 bond pdb=" CB TRP R 120 " pdb=" CG TRP R 120 " ideal model delta sigma weight residual 1.498 1.546 -0.048 3.10e-02 1.04e+03 2.35e+00 bond pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 1.524 1.490 0.034 2.25e-02 1.98e+03 2.29e+00 bond pdb=" CB GLN G 18 " pdb=" CG GLN G 18 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" CB GLU A 318 " pdb=" CG GLU A 318 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 9104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 12177 2.63 - 5.26: 129 5.26 - 7.89: 22 7.89 - 10.51: 6 10.51 - 13.14: 5 Bond angle restraints: 12339 Sorted by residual: angle pdb=" CB MET R 219 " pdb=" CG MET R 219 " pdb=" SD MET R 219 " ideal model delta sigma weight residual 112.70 125.84 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CA LYS G 14 " pdb=" CB LYS G 14 " pdb=" CG LYS G 14 " ideal model delta sigma weight residual 114.10 122.83 -8.73 2.00e+00 2.50e-01 1.91e+01 angle pdb=" CA MET R 64 " pdb=" CB MET R 64 " pdb=" CG MET R 64 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CB PRO A 288 " pdb=" CG PRO A 288 " pdb=" CD PRO A 288 " ideal model delta sigma weight residual 106.10 94.95 11.15 3.20e+00 9.77e-02 1.21e+01 angle pdb=" CB MET S 128 " pdb=" CG MET S 128 " pdb=" SD MET S 128 " ideal model delta sigma weight residual 112.70 122.68 -9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.20: 4510 14.20 - 28.41: 589 28.41 - 42.61: 232 42.61 - 56.81: 62 56.81 - 71.01: 7 Dihedral angle restraints: 5400 sinusoidal: 2126 harmonic: 3274 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual -86.00 -31.53 -54.47 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual -86.00 -129.44 43.44 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA TYR R 266 " pdb=" C TYR R 266 " pdb=" N ALA R 267 " pdb=" CA ALA R 267 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1261 0.075 - 0.150: 136 0.150 - 0.226: 9 0.226 - 0.301: 1 0.301 - 0.376: 1 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CG LEU R 241 " pdb=" CB LEU R 241 " pdb=" CD1 LEU R 241 " pdb=" CD2 LEU R 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CG LEU A 37 " pdb=" CB LEU A 37 " pdb=" CD1 LEU A 37 " pdb=" CD2 LEU A 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 1405 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 258 " 0.021 2.00e-02 2.50e+03 1.71e-02 7.27e+00 pdb=" CG TRP A 258 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 258 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 258 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 258 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 258 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 258 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 258 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 258 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 258 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 68 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.68e+00 pdb=" CG PHE R 68 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE R 68 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 68 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE R 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 68 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 68 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO S 224 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.034 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 312 2.70 - 3.25: 9310 3.25 - 3.80: 15397 3.80 - 4.35: 19345 4.35 - 4.90: 31767 Nonbonded interactions: 76131 Sorted by model distance: nonbonded pdb=" OG SER R 97 " pdb=" O PRO R 188 " model vdw 2.151 3.040 nonbonded pdb=" O MET R 277 " pdb=" OG SER R 280 " model vdw 2.178 3.040 nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.210 3.040 nonbonded pdb=" O CYS R 104 " pdb=" OG SER R 108 " model vdw 2.220 3.040 nonbonded pdb=" O SER R 279 " pdb=" OG SER R 279 " model vdw 2.220 3.040 ... (remaining 76126 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: 1.300 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.004 0.048 9112 Z= 0.201 Angle : 0.763 13.142 12345 Z= 0.391 Chirality : 0.047 0.376 1408 Planarity : 0.005 0.059 1543 Dihedral : 15.537 71.014 3273 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.25), residues: 1111 helix: 1.54 (0.26), residues: 387 sheet: -0.72 (0.31), residues: 246 loop : -1.21 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.027 0.002 TYR B 85 PHE 0.042 0.002 PHE R 68 TRP 0.046 0.003 TRP A 258 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9109) covalent geometry : angle 0.75985 (12339) SS BOND : bond 0.00657 ( 3) SS BOND : angle 3.15402 ( 6) hydrogen bonds : bond 0.09387 ( 446) hydrogen bonds : angle 6.07290 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7712 (tppt) REVERT: B 188 MET cc_start: 0.7358 (mmm) cc_final: 0.7119 (mmt) REVERT: B 254 ASP cc_start: 0.7615 (p0) cc_final: 0.7363 (p0) REVERT: B 271 CYS cc_start: 0.6817 (m) cc_final: 0.6537 (p) REVERT: B 314 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6986 (mmt90) REVERT: R 261 TRP cc_start: 0.7252 (t-100) cc_final: 0.6475 (t-100) REVERT: S 167 GLN cc_start: 0.7881 (tp40) cc_final: 0.7411 (tp40) REVERT: S 198 THR cc_start: 0.7377 (t) cc_final: 0.6843 (m) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1170 time to fit residues: 37.0775 Evaluate side-chains 237 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 36 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133653 restraints weight = 14452.545| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.90 r_work: 0.3638 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9112 Z= 0.183 Angle : 0.638 9.590 12345 Z= 0.332 Chirality : 0.044 0.285 1408 Planarity : 0.005 0.058 1543 Dihedral : 5.141 60.902 1238 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.98 % Allowed : 24.80 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.25), residues: 1111 helix: 1.69 (0.26), residues: 387 sheet: -0.54 (0.32), residues: 224 loop : -1.18 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.022 0.002 TYR R 266 PHE 0.032 0.002 PHE R 68 TRP 0.016 0.002 TRP A 258 HIS 0.005 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9109) covalent geometry : angle 0.63675 (12339) SS BOND : bond 0.00506 ( 3) SS BOND : angle 2.20638 ( 6) hydrogen bonds : bond 0.04043 ( 446) hydrogen bonds : angle 5.37618 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7370 (ttpp) REVERT: A 209 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7865 (mmtm) REVERT: B 52 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7332 (ptp90) REVERT: B 82 TRP cc_start: 0.8247 (m100) cc_final: 0.7800 (m100) REVERT: B 254 ASP cc_start: 0.7639 (p0) cc_final: 0.7393 (p0) REVERT: B 295 ASN cc_start: 0.7947 (m-40) cc_final: 0.7574 (m110) REVERT: G 14 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8526 (mmtt) REVERT: R 261 TRP cc_start: 0.7036 (t-100) cc_final: 0.5920 (t-100) REVERT: S 34 MET cc_start: 0.7581 (mtp) cc_final: 0.7368 (mmm) REVERT: S 38 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7604 (ttp80) REVERT: S 198 THR cc_start: 0.7316 (t) cc_final: 0.6851 (m) outliers start: 39 outliers final: 26 residues processed: 256 average time/residue: 0.1092 time to fit residues: 37.5985 Evaluate side-chains 264 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 67 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133454 restraints weight = 14329.778| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.89 r_work: 0.3646 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9112 Z= 0.158 Angle : 0.619 9.736 12345 Z= 0.320 Chirality : 0.043 0.313 1408 Planarity : 0.004 0.058 1543 Dihedral : 5.010 58.183 1238 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.67 % Allowed : 26.22 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.25), residues: 1111 helix: 1.75 (0.26), residues: 394 sheet: -0.58 (0.31), residues: 233 loop : -1.09 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.022 0.002 TYR R 266 PHE 0.023 0.002 PHE R 68 TRP 0.011 0.002 TRP B 99 HIS 0.006 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9109) covalent geometry : angle 0.61787 (12339) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.75041 ( 6) hydrogen bonds : bond 0.03799 ( 446) hydrogen bonds : angle 5.17481 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 186 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 171 ILE cc_start: 0.7613 (mm) cc_final: 0.7409 (mm) REVERT: B 295 ASN cc_start: 0.7900 (m-40) cc_final: 0.7646 (m110) REVERT: G 14 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8433 (mmtt) REVERT: G 48 ASP cc_start: 0.7445 (t0) cc_final: 0.7232 (t0) REVERT: S 38 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7561 (ttp80) REVERT: S 198 THR cc_start: 0.7291 (t) cc_final: 0.6792 (m) outliers start: 36 outliers final: 22 residues processed: 256 average time/residue: 0.1038 time to fit residues: 36.0449 Evaluate side-chains 259 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133781 restraints weight = 14528.089| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.90 r_work: 0.3647 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9112 Z= 0.174 Angle : 0.624 10.178 12345 Z= 0.322 Chirality : 0.044 0.318 1408 Planarity : 0.004 0.057 1543 Dihedral : 5.034 58.689 1238 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.51 % Allowed : 25.61 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.25), residues: 1111 helix: 1.81 (0.26), residues: 387 sheet: -0.56 (0.31), residues: 232 loop : -1.10 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.020 0.002 TYR R 266 PHE 0.018 0.002 PHE R 68 TRP 0.012 0.002 TRP B 99 HIS 0.005 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9109) covalent geometry : angle 0.62259 (12339) SS BOND : bond 0.00364 ( 3) SS BOND : angle 1.75729 ( 6) hydrogen bonds : bond 0.03769 ( 446) hydrogen bonds : angle 5.16071 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 0.387 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 33 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 295 ASN cc_start: 0.7925 (m-40) cc_final: 0.7698 (m-40) REVERT: B 318 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7608 (tt) REVERT: G 14 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8449 (mmtt) REVERT: R 57 PHE cc_start: 0.6684 (m-10) cc_final: 0.6427 (m-10) REVERT: R 261 TRP cc_start: 0.7020 (t-100) cc_final: 0.5941 (t-100) REVERT: S 38 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7574 (ttp80) REVERT: S 168 ARG cc_start: 0.8665 (ttm170) cc_final: 0.8056 (mtt-85) REVERT: S 198 THR cc_start: 0.7320 (t) cc_final: 0.6818 (m) outliers start: 54 outliers final: 38 residues processed: 277 average time/residue: 0.1104 time to fit residues: 41.2632 Evaluate side-chains 280 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.159324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135725 restraints weight = 14459.119| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.93 r_work: 0.3674 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9112 Z= 0.128 Angle : 0.598 10.186 12345 Z= 0.308 Chirality : 0.042 0.168 1408 Planarity : 0.004 0.057 1543 Dihedral : 4.894 58.609 1238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.39 % Allowed : 27.45 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1111 helix: 1.85 (0.26), residues: 394 sheet: -0.45 (0.31), residues: 229 loop : -1.05 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.022 0.001 TYR R 266 PHE 0.014 0.001 PHE R 68 TRP 0.012 0.001 TRP A 258 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9109) covalent geometry : angle 0.59725 (12339) SS BOND : bond 0.00345 ( 3) SS BOND : angle 1.70609 ( 6) hydrogen bonds : bond 0.03504 ( 446) hydrogen bonds : angle 5.00919 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.362 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: symmetry clash REVERT: A 33 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 199 PHE cc_start: 0.7996 (m-80) cc_final: 0.7514 (m-80) REVERT: A 210 LYS cc_start: 0.6763 (tppp) cc_final: 0.6159 (ttmt) REVERT: A 258 TRP cc_start: 0.5992 (m100) cc_final: 0.5595 (m100) REVERT: B 33 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7433 (pt) REVERT: B 172 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6901 (tm-30) REVERT: B 283 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7903 (tpp80) REVERT: B 318 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7606 (tt) REVERT: G 14 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8506 (mmtt) REVERT: R 57 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6348 (m-10) REVERT: S 20 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7596 (mp) REVERT: S 38 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7521 (ttp80) REVERT: S 128 MET cc_start: 0.7870 (mmm) cc_final: 0.6791 (mmm) REVERT: S 147 CYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4693 (t) REVERT: S 168 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8157 (mtt-85) outliers start: 43 outliers final: 29 residues processed: 264 average time/residue: 0.1066 time to fit residues: 38.4008 Evaluate side-chains 272 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 113 HIS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 217 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133776 restraints weight = 14492.033| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.90 r_work: 0.3645 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9112 Z= 0.182 Angle : 0.632 11.556 12345 Z= 0.326 Chirality : 0.043 0.166 1408 Planarity : 0.004 0.068 1543 Dihedral : 4.995 57.834 1238 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.49 % Allowed : 27.04 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1111 helix: 1.91 (0.26), residues: 389 sheet: -0.53 (0.30), residues: 247 loop : -1.05 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.025 0.002 TYR B 85 PHE 0.015 0.002 PHE B 199 TRP 0.011 0.002 TRP S 36 HIS 0.005 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9109) covalent geometry : angle 0.63111 (12339) SS BOND : bond 0.00276 ( 3) SS BOND : angle 1.62768 ( 6) hydrogen bonds : bond 0.03726 ( 446) hydrogen bonds : angle 5.15378 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 214 CYS cc_start: 0.7563 (m) cc_final: 0.7331 (m) REVERT: B 33 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7451 (pt) REVERT: B 172 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6900 (tm-30) REVERT: B 283 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7819 (tpp80) REVERT: B 295 ASN cc_start: 0.7865 (m-40) cc_final: 0.7592 (m110) REVERT: B 318 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7417 (tt) REVERT: G 14 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8604 (mmtt) REVERT: R 57 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6324 (m-10) REVERT: R 261 TRP cc_start: 0.7049 (t-100) cc_final: 0.5961 (t-100) REVERT: S 20 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7563 (mp) REVERT: S 38 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7535 (ttp80) REVERT: S 128 MET cc_start: 0.7862 (mmm) cc_final: 0.7412 (mmm) REVERT: S 168 ARG cc_start: 0.8700 (ttm170) cc_final: 0.8092 (mtt-85) outliers start: 44 outliers final: 31 residues processed: 273 average time/residue: 0.1096 time to fit residues: 40.6011 Evaluate side-chains 278 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 113 HIS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 76 optimal weight: 0.0670 chunk 100 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134974 restraints weight = 14670.570| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.97 r_work: 0.3661 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9112 Z= 0.134 Angle : 0.625 10.279 12345 Z= 0.319 Chirality : 0.043 0.164 1408 Planarity : 0.004 0.059 1543 Dihedral : 4.909 58.494 1238 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.39 % Allowed : 27.24 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1111 helix: 1.95 (0.26), residues: 389 sheet: -0.50 (0.31), residues: 235 loop : -0.93 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.024 0.001 TYR R 266 PHE 0.017 0.001 PHE S 68 TRP 0.028 0.002 TRP A 258 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9109) covalent geometry : angle 0.62248 (12339) SS BOND : bond 0.00419 ( 3) SS BOND : angle 2.52891 ( 6) hydrogen bonds : bond 0.03479 ( 446) hydrogen bonds : angle 5.03473 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 199 PHE cc_start: 0.7996 (m-80) cc_final: 0.7542 (m-80) REVERT: B 33 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7471 (pt) REVERT: B 172 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6892 (tm-30) REVERT: B 283 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7901 (tpp80) REVERT: B 295 ASN cc_start: 0.7830 (m-40) cc_final: 0.7551 (m-40) REVERT: B 314 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7081 (mmt90) REVERT: B 318 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7620 (tt) REVERT: G 14 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8580 (mmtt) REVERT: R 43 MET cc_start: 0.6435 (mtm) cc_final: 0.6160 (mtm) REVERT: R 57 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6313 (m-10) REVERT: S 20 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7636 (mp) REVERT: S 38 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7535 (ttp80) REVERT: S 168 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8231 (mtt-85) outliers start: 43 outliers final: 35 residues processed: 261 average time/residue: 0.1095 time to fit residues: 38.7932 Evaluate side-chains 276 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 113 HIS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 0.0570 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134048 restraints weight = 14449.504| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.90 r_work: 0.3647 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9112 Z= 0.171 Angle : 0.654 10.921 12345 Z= 0.334 Chirality : 0.045 0.264 1408 Planarity : 0.004 0.065 1543 Dihedral : 4.997 58.004 1238 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.69 % Allowed : 26.84 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.26), residues: 1111 helix: 2.01 (0.26), residues: 387 sheet: -0.53 (0.31), residues: 241 loop : -0.99 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.021 0.002 TYR R 266 PHE 0.028 0.002 PHE S 68 TRP 0.041 0.002 TRP A 258 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9109) covalent geometry : angle 0.65168 (12339) SS BOND : bond 0.00627 ( 3) SS BOND : angle 2.77200 ( 6) hydrogen bonds : bond 0.03639 ( 446) hydrogen bonds : angle 5.09313 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 214 CYS cc_start: 0.7614 (m) cc_final: 0.7381 (m) REVERT: A 337 ASP cc_start: 0.7777 (m-30) cc_final: 0.7576 (m-30) REVERT: B 33 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7488 (pt) REVERT: B 172 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6919 (tm-30) REVERT: B 283 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7826 (tpp80) REVERT: B 289 TYR cc_start: 0.8180 (m-80) cc_final: 0.7859 (m-80) REVERT: B 295 ASN cc_start: 0.7840 (m-40) cc_final: 0.7378 (m-40) REVERT: B 318 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7430 (tt) REVERT: G 14 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8643 (mmtt) REVERT: R 43 MET cc_start: 0.6772 (mtm) cc_final: 0.6486 (mtm) REVERT: R 57 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6305 (m-10) REVERT: S 38 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7620 (ttp80) REVERT: S 168 ARG cc_start: 0.8737 (ttm170) cc_final: 0.8164 (mtt-85) outliers start: 46 outliers final: 34 residues processed: 267 average time/residue: 0.1072 time to fit residues: 39.0737 Evaluate side-chains 275 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 113 HIS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 0.0170 chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.159735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135943 restraints weight = 14603.685| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.95 r_work: 0.3667 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9112 Z= 0.132 Angle : 0.658 12.255 12345 Z= 0.334 Chirality : 0.045 0.292 1408 Planarity : 0.004 0.061 1543 Dihedral : 4.935 58.476 1238 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.78 % Allowed : 27.96 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1111 helix: 2.04 (0.26), residues: 387 sheet: -0.41 (0.32), residues: 237 loop : -0.95 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 314 TYR 0.023 0.001 TYR R 266 PHE 0.013 0.002 PHE S 68 TRP 0.028 0.002 TRP A 258 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9109) covalent geometry : angle 0.65630 (12339) SS BOND : bond 0.00461 ( 3) SS BOND : angle 2.50865 ( 6) hydrogen bonds : bond 0.03514 ( 446) hydrogen bonds : angle 5.05914 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 258 TRP cc_start: 0.6220 (m100) cc_final: 0.5410 (m100) REVERT: B 33 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7423 (pt) REVERT: B 172 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6902 (tm-30) REVERT: B 283 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7830 (tpp80) REVERT: B 289 TYR cc_start: 0.8015 (m-80) cc_final: 0.7613 (m-80) REVERT: B 295 ASN cc_start: 0.7803 (m-40) cc_final: 0.7283 (m-40) REVERT: B 318 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7616 (tt) REVERT: G 14 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8625 (mmtt) REVERT: G 18 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7728 (tm-30) REVERT: R 43 MET cc_start: 0.6602 (mtm) cc_final: 0.6217 (mtm) REVERT: R 57 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.6281 (m-10) REVERT: S 38 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7595 (ttp80) REVERT: S 168 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8172 (mtt-85) outliers start: 37 outliers final: 31 residues processed: 264 average time/residue: 0.1068 time to fit residues: 38.3482 Evaluate side-chains 269 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 113 HIS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.157435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133644 restraints weight = 14560.605| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.91 r_work: 0.3640 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9112 Z= 0.205 Angle : 0.698 11.938 12345 Z= 0.358 Chirality : 0.046 0.289 1408 Planarity : 0.005 0.063 1543 Dihedral : 5.157 57.598 1238 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.98 % Allowed : 28.37 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.23 (0.26), residues: 1111 helix: 1.96 (0.26), residues: 387 sheet: -0.47 (0.31), residues: 253 loop : -1.02 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.032 0.002 TYR B 85 PHE 0.020 0.002 PHE B 151 TRP 0.033 0.002 TRP R 257 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9109) covalent geometry : angle 0.69586 (12339) SS BOND : bond 0.00563 ( 3) SS BOND : angle 2.64060 ( 6) hydrogen bonds : bond 0.03826 ( 446) hydrogen bonds : angle 5.24023 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 214 CYS cc_start: 0.7596 (m) cc_final: 0.7357 (m) REVERT: B 33 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7496 (pt) REVERT: B 172 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 232 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7930 (tp) REVERT: B 283 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7832 (tpp80) REVERT: B 289 TYR cc_start: 0.8125 (m-80) cc_final: 0.7834 (m-80) REVERT: G 14 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8622 (mmtt) REVERT: R 43 MET cc_start: 0.6493 (mtm) cc_final: 0.6214 (mtm) REVERT: R 57 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6454 (m-10) REVERT: R 261 TRP cc_start: 0.7021 (t-100) cc_final: 0.6073 (t-100) REVERT: S 38 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7607 (ttp80) REVERT: S 168 ARG cc_start: 0.8732 (ttm170) cc_final: 0.8192 (mtt-85) outliers start: 39 outliers final: 31 residues processed: 265 average time/residue: 0.1081 time to fit residues: 39.0967 Evaluate side-chains 274 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 113 HIS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134543 restraints weight = 14402.705| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.91 r_work: 0.3649 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9112 Z= 0.177 Angle : 0.702 12.418 12345 Z= 0.356 Chirality : 0.046 0.303 1408 Planarity : 0.004 0.060 1543 Dihedral : 5.158 58.146 1238 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.67 % Allowed : 28.67 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.19 (0.26), residues: 1111 helix: 1.93 (0.26), residues: 387 sheet: -0.50 (0.31), residues: 252 loop : -1.04 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.024 0.002 TYR B 85 PHE 0.017 0.002 PHE B 151 TRP 0.030 0.002 TRP R 257 HIS 0.005 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9109) covalent geometry : angle 0.70011 (12339) SS BOND : bond 0.00516 ( 3) SS BOND : angle 2.56248 ( 6) hydrogen bonds : bond 0.03740 ( 446) hydrogen bonds : angle 5.23789 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.61 seconds wall clock time: 41 minutes 13.56 seconds (2473.56 seconds total)