Starting phenix.real_space_refine on Mon May 12 11:01:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpe_62485/05_2025/9kpe_62485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpe_62485/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9kpe_62485/05_2025/9kpe_62485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpe_62485/05_2025/9kpe_62485.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpe_62485/05_2025/9kpe_62485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpe_62485/05_2025/9kpe_62485.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.23, per 1000 atoms: 0.59 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: 2.22 Conformation dependent library (CDL) restraints added in 976.3 milliseconds 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: 0.89 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: 2.60 Time building geometry restraints manager: 2.60 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: 1.010 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.650 ------------------------------------------------------------------------------- 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 : 20.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (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 TRP 0.046 0.003 TRP A 258 HIS 0.006 0.001 HIS B 54 PHE 0.042 0.002 PHE R 68 TYR 0.027 0.002 TYR B 85 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.09387 ( 446) hydrogen bonds : angle 6.07290 ( 1269) SS BOND : bond 0.00657 ( 3) SS BOND : angle 3.15402 ( 6) covalent geometry : bond 0.00435 ( 9109) covalent geometry : angle 0.75985 (12339) *********************** 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 : 1.079 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: 0.2325 time to fit residues: 73.6459 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 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 = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133718 restraints weight = 14349.016| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.88 r_work: 0.3648 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 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 : 14.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (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 TRP 0.016 0.002 TRP A 258 HIS 0.005 0.001 HIS S 155 PHE 0.032 0.002 PHE R 68 TYR 0.022 0.002 TYR R 266 ARG 0.005 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 446) hydrogen bonds : angle 5.37618 ( 1269) SS BOND : bond 0.00506 ( 3) SS BOND : angle 2.20638 ( 6) covalent geometry : bond 0.00396 ( 9109) covalent geometry : angle 0.63675 (12339) *********************** 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 : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7702 (ttpp) cc_final: 0.7369 (ttpp) REVERT: A 209 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7864 (mmtm) REVERT: B 52 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7344 (ptp90) REVERT: B 82 TRP cc_start: 0.8244 (m100) cc_final: 0.7798 (m100) REVERT: B 254 ASP cc_start: 0.7632 (p0) cc_final: 0.7381 (p0) REVERT: B 295 ASN cc_start: 0.7948 (m-40) cc_final: 0.7565 (m110) REVERT: G 14 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8527 (mmtt) REVERT: R 261 TRP cc_start: 0.7020 (t-100) cc_final: 0.5896 (t-100) REVERT: S 34 MET cc_start: 0.7589 (mtp) cc_final: 0.7371 (mmm) REVERT: S 38 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7601 (ttp80) REVERT: S 198 THR cc_start: 0.7316 (t) cc_final: 0.6848 (m) outliers start: 39 outliers final: 26 residues processed: 256 average time/residue: 0.2283 time to fit residues: 78.0701 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 : 0.951 ------------------------------------------------------------------------------- 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 89 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4039 r_free = 0.4039 target = 0.154231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130275 restraints weight = 14462.279| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.86 r_work: 0.3595 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9112 Z= 0.325 Angle : 0.717 9.081 12345 Z= 0.380 Chirality : 0.048 0.301 1408 Planarity : 0.005 0.062 1543 Dihedral : 5.558 59.043 1238 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.71 % Allowed : 25.00 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1111 helix: 1.30 (0.25), residues: 391 sheet: -0.79 (0.30), residues: 244 loop : -1.26 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.008 0.002 HIS B 91 PHE 0.028 0.002 PHE B 199 TYR 0.028 0.003 TYR B 85 ARG 0.004 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 446) hydrogen bonds : angle 5.59215 ( 1269) SS BOND : bond 0.00423 ( 3) SS BOND : angle 1.92052 ( 6) covalent geometry : bond 0.00685 ( 9109) covalent geometry : angle 0.71555 (12339) *********************** 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 316 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7284 (m-40) cc_final: 0.6995 (m-40) REVERT: A 211 TRP cc_start: 0.6656 (p-90) cc_final: 0.6399 (p-90) REVERT: A 214 CYS cc_start: 0.7621 (m) cc_final: 0.7369 (m) REVERT: A 337 ASP cc_start: 0.7829 (m-30) cc_final: 0.7576 (m-30) REVERT: B 52 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7646 (ptp90) REVERT: B 188 MET cc_start: 0.7435 (mmm) cc_final: 0.7118 (mmt) REVERT: B 254 ASP cc_start: 0.7573 (p0) cc_final: 0.7274 (p0) REVERT: G 14 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8443 (mmtt) REVERT: G 48 ASP cc_start: 0.7512 (t0) cc_final: 0.7281 (t0) REVERT: R 234 ILE cc_start: 0.7734 (mm) cc_final: 0.7368 (mm) REVERT: R 246 THR cc_start: 0.6976 (OUTLIER) cc_final: 0.6558 (m) REVERT: R 261 TRP cc_start: 0.7002 (t-100) cc_final: 0.6265 (t-100) REVERT: S 34 MET cc_start: 0.7671 (mtp) cc_final: 0.7466 (mmm) REVERT: S 98 ARG cc_start: 0.7954 (ptt180) cc_final: 0.7668 (ptt180) REVERT: S 227 PHE cc_start: 0.7872 (m-80) cc_final: 0.7551 (m-10) outliers start: 56 outliers final: 41 residues processed: 284 average time/residue: 0.2151 time to fit residues: 82.6679 Evaluate side-chains 295 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE 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 320 TYR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 90 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 192 LEU 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 252 LEU Chi-restraints excluded: chain B residue 264 TYR 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 11 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 117 LEU 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 218 MET Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4063 r_free = 0.4063 target = 0.155997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132125 restraints weight = 14379.760| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.87 r_work: 0.3621 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9112 Z= 0.201 Angle : 0.638 9.534 12345 Z= 0.334 Chirality : 0.045 0.294 1408 Planarity : 0.005 0.054 1543 Dihedral : 5.277 58.788 1238 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.00 % Allowed : 26.43 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1111 helix: 1.51 (0.26), residues: 393 sheet: -0.80 (0.30), residues: 252 loop : -1.10 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.007 0.001 HIS S 155 PHE 0.017 0.002 PHE R 68 TYR 0.028 0.002 TYR B 85 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 446) hydrogen bonds : angle 5.41662 ( 1269) SS BOND : bond 0.00357 ( 3) SS BOND : angle 1.83685 ( 6) covalent geometry : bond 0.00435 ( 9109) covalent geometry : angle 0.63655 (12339) *********************** 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: 49 poor density : 255 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 CYS cc_start: 0.7630 (m) cc_final: 0.7336 (m) REVERT: A 337 ASP cc_start: 0.7806 (m-30) cc_final: 0.7565 (m-30) REVERT: B 52 ARG cc_start: 0.7808 (ptp90) cc_final: 0.7534 (ptp90) REVERT: B 188 MET cc_start: 0.7386 (mmm) cc_final: 0.7108 (mmt) REVERT: B 198 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7402 (mt) REVERT: B 254 ASP cc_start: 0.7530 (p0) cc_final: 0.7282 (p0) REVERT: B 283 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7882 (tpp80) REVERT: B 293 ASN cc_start: 0.7273 (p0) cc_final: 0.6962 (p0) REVERT: B 295 ASN cc_start: 0.7944 (m-40) cc_final: 0.7459 (m-40) REVERT: G 14 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8463 (mmtt) REVERT: G 48 ASP cc_start: 0.7499 (t0) cc_final: 0.7238 (t0) REVERT: R 43 MET cc_start: 0.6652 (mtm) cc_final: 0.6393 (mtm) REVERT: R 57 PHE cc_start: 0.6692 (m-10) cc_final: 0.6476 (m-10) REVERT: R 261 TRP cc_start: 0.7004 (t-100) cc_final: 0.6229 (t-100) REVERT: S 20 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7781 (mp) REVERT: S 34 MET cc_start: 0.7627 (mtp) cc_final: 0.7388 (mmm) REVERT: S 38 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7569 (ttp80) REVERT: S 198 THR cc_start: 0.7389 (t) cc_final: 0.6900 (m) outliers start: 49 outliers final: 31 residues processed: 283 average time/residue: 0.2244 time to fit residues: 85.0358 Evaluate side-chains 284 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain A residue 269 ASN 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 B residue 54 HIS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL 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 243 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 G residue 54 VAL 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 100 THR 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 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 117 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 176 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.156514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132675 restraints weight = 14407.686| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.87 r_work: 0.3636 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9112 Z= 0.178 Angle : 0.629 10.028 12345 Z= 0.326 Chirality : 0.044 0.323 1408 Planarity : 0.004 0.056 1543 Dihedral : 5.172 58.967 1238 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.92 % Allowed : 25.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1111 helix: 1.64 (0.26), residues: 393 sheet: -0.75 (0.30), residues: 250 loop : -1.08 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 258 HIS 0.007 0.001 HIS B 183 PHE 0.020 0.002 PHE S 68 TYR 0.029 0.002 TYR B 85 ARG 0.005 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 446) hydrogen bonds : angle 5.30006 ( 1269) SS BOND : bond 0.00355 ( 3) SS BOND : angle 1.78117 ( 6) covalent geometry : bond 0.00387 ( 9109) covalent geometry : angle 0.62764 (12339) *********************** 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 307 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 CYS cc_start: 0.7623 (m) cc_final: 0.7321 (m) REVERT: A 249 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7697 (mp) REVERT: B 52 ARG cc_start: 0.7746 (ptp90) cc_final: 0.7511 (ptp90) REVERT: B 188 MET cc_start: 0.7402 (mmm) cc_final: 0.7122 (mmt) REVERT: B 254 ASP cc_start: 0.7527 (p0) cc_final: 0.7283 (p0) REVERT: B 283 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7791 (tpp80) REVERT: G 14 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8527 (mmtt) REVERT: G 48 ASP cc_start: 0.7473 (t0) cc_final: 0.7213 (t0) REVERT: R 43 MET cc_start: 0.6756 (mtm) cc_final: 0.6407 (mtm) REVERT: R 57 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6345 (m-10) REVERT: R 246 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6443 (m) REVERT: R 261 TRP cc_start: 0.7044 (t-100) cc_final: 0.5788 (t-100) REVERT: S 20 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7765 (mp) REVERT: S 38 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7630 (ttp80) REVERT: S 128 MET cc_start: 0.7806 (mmm) cc_final: 0.7158 (mmm) REVERT: S 168 ARG cc_start: 0.8716 (ttm170) cc_final: 0.8076 (mtt-85) outliers start: 58 outliers final: 39 residues processed: 282 average time/residue: 0.2225 time to fit residues: 84.5279 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 : 0.938 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL 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 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 192 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 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 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 100 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 246 THR 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 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN ** 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 = 0.4078 r_free = 0.4078 target = 0.157287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133447 restraints weight = 14364.575| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.88 r_work: 0.3636 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1523 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= 0.169 Angle : 0.627 10.516 12345 Z= 0.324 Chirality : 0.044 0.277 1408 Planarity : 0.004 0.064 1543 Dihedral : 5.123 58.783 1238 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.20 % Allowed : 25.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1111 helix: 1.72 (0.26), residues: 393 sheet: -0.72 (0.30), residues: 247 loop : -1.06 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 257 HIS 0.006 0.001 HIS S 155 PHE 0.017 0.002 PHE A 336 TYR 0.031 0.002 TYR B 85 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 446) hydrogen bonds : angle 5.25760 ( 1269) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.65245 ( 6) covalent geometry : bond 0.00370 ( 9109) covalent geometry : angle 0.62589 (12339) *********************** 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 298 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 CYS cc_start: 0.7585 (m) cc_final: 0.7317 (m) REVERT: B 172 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6931 (tm-30) REVERT: B 188 MET cc_start: 0.7229 (mmm) cc_final: 0.6987 (mmt) REVERT: B 220 GLN cc_start: 0.7232 (mt0) cc_final: 0.6877 (mt0) REVERT: B 254 ASP cc_start: 0.7516 (p0) cc_final: 0.7279 (p0) REVERT: B 283 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7908 (tpp80) REVERT: B 318 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7452 (tt) REVERT: G 14 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8559 (mmtt) REVERT: G 48 ASP cc_start: 0.7466 (t0) cc_final: 0.7185 (t0) REVERT: R 43 MET cc_start: 0.6547 (mtm) cc_final: 0.6237 (mtm) REVERT: R 57 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6314 (m-10) REVERT: R 261 TRP cc_start: 0.7047 (t-100) cc_final: 0.6065 (t-100) REVERT: S 20 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7727 (mp) REVERT: S 38 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7624 (ttp80) REVERT: S 83 MET cc_start: 0.6078 (mtp) cc_final: 0.5699 (mtp) REVERT: S 128 MET cc_start: 0.7764 (mmm) cc_final: 0.7284 (mmm) REVERT: S 168 ARG cc_start: 0.8700 (ttm170) cc_final: 0.8064 (mtt-85) REVERT: S 218 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7466 (ttt) outliers start: 51 outliers final: 36 residues processed: 276 average time/residue: 0.2146 time to fit residues: 79.7680 Evaluate side-chains 285 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ASP 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 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 181 THR Chi-restraints excluded: chain B residue 192 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 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 100 THR 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 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4078 r_free = 0.4078 target = 0.157643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133600 restraints weight = 14508.968| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.92 r_work: 0.3644 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9112 Z= 0.167 Angle : 0.648 10.507 12345 Z= 0.332 Chirality : 0.045 0.340 1408 Planarity : 0.004 0.058 1543 Dihedral : 5.095 58.762 1238 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.10 % Allowed : 26.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1111 helix: 1.76 (0.26), residues: 395 sheet: -0.70 (0.31), residues: 249 loop : -1.04 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 257 HIS 0.005 0.001 HIS S 155 PHE 0.014 0.002 PHE A 336 TYR 0.046 0.002 TYR B 85 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 446) hydrogen bonds : angle 5.22753 ( 1269) SS BOND : bond 0.00479 ( 3) SS BOND : angle 2.56595 ( 6) covalent geometry : bond 0.00365 ( 9109) covalent geometry : angle 0.64569 (12339) *********************** 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 298 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 CYS cc_start: 0.7663 (m) cc_final: 0.7360 (m) REVERT: B 172 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6951 (tm-30) REVERT: B 188 MET cc_start: 0.7242 (mmm) cc_final: 0.6986 (mmt) REVERT: B 220 GLN cc_start: 0.7263 (mt0) cc_final: 0.6891 (mt0) REVERT: B 254 ASP cc_start: 0.7551 (p0) cc_final: 0.7301 (p0) REVERT: B 283 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7910 (tpp80) REVERT: B 289 TYR cc_start: 0.8096 (m-80) cc_final: 0.7857 (m-80) REVERT: B 318 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7464 (tt) REVERT: G 14 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8610 (mmtt) REVERT: R 43 MET cc_start: 0.6563 (mtm) cc_final: 0.6257 (mtm) REVERT: R 57 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6288 (m-10) REVERT: R 261 TRP cc_start: 0.7095 (t-100) cc_final: 0.6086 (t-100) REVERT: S 20 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7728 (mp) REVERT: S 38 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7623 (ttp80) REVERT: S 83 MET cc_start: 0.6180 (mtp) cc_final: 0.5964 (mtp) REVERT: S 168 ARG cc_start: 0.8712 (ttm170) cc_final: 0.8110 (mtt-85) outliers start: 50 outliers final: 38 residues processed: 277 average time/residue: 0.2131 time to fit residues: 80.0014 Evaluate side-chains 286 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 54 LYS 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 303 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL 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 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 218 CYS 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 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 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4084 r_free = 0.4084 target = 0.158011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134045 restraints weight = 14644.346| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.93 r_work: 0.3647 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9112 Z= 0.159 Angle : 0.647 10.613 12345 Z= 0.330 Chirality : 0.044 0.204 1408 Planarity : 0.004 0.062 1543 Dihedral : 5.068 58.715 1238 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.29 % Allowed : 27.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1111 helix: 1.86 (0.26), residues: 393 sheet: -0.64 (0.31), residues: 240 loop : -1.06 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 257 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE B 151 TYR 0.037 0.002 TYR B 85 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 446) hydrogen bonds : angle 5.20102 ( 1269) SS BOND : bond 0.00602 ( 3) SS BOND : angle 2.67074 ( 6) covalent geometry : bond 0.00353 ( 9109) covalent geometry : angle 0.64426 (12339) *********************** 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 286 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 CYS cc_start: 0.7620 (m) cc_final: 0.7344 (m) REVERT: B 55 LEU cc_start: 0.8289 (mm) cc_final: 0.7992 (mm) REVERT: B 172 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6969 (tm-30) REVERT: B 188 MET cc_start: 0.7169 (mmm) cc_final: 0.6899 (mmt) REVERT: B 220 GLN cc_start: 0.7254 (mt0) cc_final: 0.6881 (mt0) REVERT: B 254 ASP cc_start: 0.7501 (p0) cc_final: 0.7260 (p0) REVERT: B 283 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7917 (tpp80) REVERT: B 289 TYR cc_start: 0.8021 (m-80) cc_final: 0.7721 (m-80) REVERT: B 318 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7450 (tt) REVERT: G 14 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8597 (mmtt) REVERT: R 43 MET cc_start: 0.6539 (mtm) cc_final: 0.6223 (mtm) REVERT: R 57 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6258 (m-10) REVERT: R 261 TRP cc_start: 0.7072 (t-100) cc_final: 0.5994 (t-100) REVERT: R 264 PHE cc_start: 0.6966 (t80) cc_final: 0.6682 (t80) REVERT: R 268 PHE cc_start: 0.8015 (m-80) cc_final: 0.7766 (m-80) REVERT: S 20 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7716 (mp) REVERT: S 38 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7702 (ttp80) REVERT: S 168 ARG cc_start: 0.8729 (ttm170) cc_final: 0.8153 (mtt-85) outliers start: 42 outliers final: 34 residues processed: 267 average time/residue: 0.2114 time to fit residues: 76.1970 Evaluate side-chains 282 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL 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 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 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 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 20 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4064 r_free = 0.4064 target = 0.156435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132414 restraints weight = 14536.936| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.91 r_work: 0.3616 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9112 Z= 0.240 Angle : 0.705 10.882 12345 Z= 0.363 Chirality : 0.046 0.240 1408 Planarity : 0.005 0.059 1543 Dihedral : 5.295 58.607 1238 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.49 % Allowed : 27.55 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1111 helix: 1.84 (0.26), residues: 387 sheet: -0.71 (0.31), residues: 248 loop : -1.16 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 257 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE B 199 TYR 0.049 0.002 TYR B 85 ARG 0.006 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 446) hydrogen bonds : angle 5.35707 ( 1269) SS BOND : bond 0.00634 ( 3) SS BOND : angle 2.69425 ( 6) covalent geometry : bond 0.00519 ( 9109) covalent geometry : angle 0.70246 (12339) *********************** 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 298 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.995 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 337 ASP cc_start: 0.7790 (m-30) cc_final: 0.7526 (m-30) REVERT: B 55 LEU cc_start: 0.8320 (mm) cc_final: 0.8031 (mm) REVERT: B 172 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 188 MET cc_start: 0.7254 (mmm) cc_final: 0.6978 (mmt) REVERT: B 254 ASP cc_start: 0.7462 (p0) cc_final: 0.7198 (p0) REVERT: B 283 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7827 (tpp80) REVERT: B 289 TYR cc_start: 0.8089 (m-80) cc_final: 0.7837 (m-80) REVERT: B 314 ARG cc_start: 0.7639 (mmt90) cc_final: 0.7297 (mmt90) REVERT: B 318 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7504 (tt) REVERT: G 14 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8598 (mmtt) REVERT: G 47 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6569 (mm-30) REVERT: R 43 MET cc_start: 0.6610 (mtm) cc_final: 0.6295 (mtm) REVERT: R 57 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: R 68 PHE cc_start: 0.4021 (OUTLIER) cc_final: 0.3697 (p90) REVERT: R 192 PHE cc_start: 0.6532 (t80) cc_final: 0.6248 (t80) REVERT: R 261 TRP cc_start: 0.7084 (t-100) cc_final: 0.6303 (t-100) REVERT: R 264 PHE cc_start: 0.6962 (t80) cc_final: 0.6730 (t80) REVERT: S 20 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7693 (mp) REVERT: S 168 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8138 (mtt-85) outliers start: 44 outliers final: 35 residues processed: 281 average time/residue: 0.2160 time to fit residues: 81.7235 Evaluate side-chains 302 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ASP 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 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 243 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 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 68 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 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 109 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.158049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134104 restraints weight = 14573.248| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.94 r_work: 0.3657 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9112 Z= 0.158 Angle : 0.670 12.445 12345 Z= 0.340 Chirality : 0.045 0.274 1408 Planarity : 0.004 0.060 1543 Dihedral : 5.155 58.602 1238 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1111 helix: 1.95 (0.26), residues: 387 sheet: -0.67 (0.32), residues: 240 loop : -1.09 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 211 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE S 68 TYR 0.032 0.002 TYR B 85 ARG 0.007 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 446) hydrogen bonds : angle 5.23052 ( 1269) SS BOND : bond 0.00512 ( 3) SS BOND : angle 2.55885 ( 6) covalent geometry : bond 0.00350 ( 9109) covalent geometry : angle 0.66785 (12339) ********************** 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 290 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7271 (tttt) REVERT: A 214 CYS cc_start: 0.7670 (m) cc_final: 0.7385 (m) REVERT: B 55 LEU cc_start: 0.8258 (mm) cc_final: 0.7952 (mm) REVERT: B 172 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6923 (tm-30) REVERT: B 188 MET cc_start: 0.7140 (mmm) cc_final: 0.6869 (mmt) REVERT: B 220 GLN cc_start: 0.7262 (mt0) cc_final: 0.6868 (mt0) REVERT: B 254 ASP cc_start: 0.7456 (p0) cc_final: 0.7245 (p0) REVERT: B 283 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7802 (tpp80) REVERT: B 289 TYR cc_start: 0.8005 (m-80) cc_final: 0.7758 (m-80) REVERT: B 318 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7362 (tt) REVERT: G 14 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8573 (mmtt) REVERT: G 18 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7629 (tm-30) REVERT: R 43 MET cc_start: 0.6510 (mtm) cc_final: 0.6196 (mtm) REVERT: R 57 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6248 (m-10) REVERT: R 68 PHE cc_start: 0.3937 (OUTLIER) cc_final: 0.3619 (p90) REVERT: R 261 TRP cc_start: 0.7038 (t-100) cc_final: 0.6010 (t-100) REVERT: R 264 PHE cc_start: 0.6916 (t80) cc_final: 0.6617 (t80) REVERT: S 20 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7679 (mp) REVERT: S 83 MET cc_start: 0.6000 (mtp) cc_final: 0.5383 (mtp) REVERT: S 168 ARG cc_start: 0.8742 (ttm170) cc_final: 0.8164 (mtt-85) outliers start: 43 outliers final: 37 residues processed: 275 average time/residue: 0.2211 time to fit residues: 81.9947 Evaluate side-chains 288 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL 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 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 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 54 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain R residue 68 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 140 THR 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 12 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4072 r_free = 0.4072 target = 0.156862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132925 restraints weight = 14564.281| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.94 r_work: 0.3638 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9112 Z= 0.198 Angle : 0.692 14.656 12345 Z= 0.352 Chirality : 0.046 0.268 1408 Planarity : 0.005 0.061 1543 Dihedral : 5.235 58.380 1238 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.49 % Allowed : 28.06 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1111 helix: 1.87 (0.26), residues: 387 sheet: -0.68 (0.31), residues: 248 loop : -1.14 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 211 HIS 0.004 0.001 HIS R 181 PHE 0.014 0.002 PHE B 151 TYR 0.040 0.002 TYR B 85 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 446) hydrogen bonds : angle 5.28671 ( 1269) SS BOND : bond 0.00559 ( 3) SS BOND : angle 2.58030 ( 6) covalent geometry : bond 0.00437 ( 9109) covalent geometry : angle 0.69015 (12339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4333.68 seconds wall clock time: 76 minutes 5.99 seconds (4565.99 seconds total)