Starting phenix.real_space_refine on Sat Jul 26 14:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7db6_30627/07_2025/7db6_30627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7db6_30627/07_2025/7db6_30627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7db6_30627/07_2025/7db6_30627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7db6_30627/07_2025/7db6_30627.map" model { file = "/net/cci-nas-00/data/ceres_data/7db6_30627/07_2025/7db6_30627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7db6_30627/07_2025/7db6_30627.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5600 2.51 5 N 1479 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8767 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2210 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'JEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.61 Number of scatterers: 8767 At special positions: 0 Unit cell: (128.246, 125.364, 89.3401, 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 62 16.00 O 1626 8.00 N 1479 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 4.268A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.798A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.586A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.781A pdb=" N LYS A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.627A pdb=" N ASN A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 4.248A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.701A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.856A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.716A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.553A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.010A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'D' and resid 24 through 51 removed outlier: 4.658A pdb=" N ALA D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N CYS D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 79 removed outlier: 4.027A pdb=" N VAL D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.551A pdb=" N ASN D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 130 removed outlier: 3.786A pdb=" N GLY D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 142 through 160 Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.757A pdb=" N VAL D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.768A pdb=" N ILE D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 4.808A pdb=" N MET D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 261 Proline residue: D 253 - end of helix Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.691A pdb=" N MET D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix No H-bonds generated for 'chain 'D' and resid 264 through 272' Processing helix chain 'D' and resid 273 through 298 removed outlier: 3.748A pdb=" N PHE D 277 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.855A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.648A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.105A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.504A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.973A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.550A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.445A 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: 6.979A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.544A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.201A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.151A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 169 through 170 381 hydrogen bonds defined for protein. 1077 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: 2.74 Time building geometry restraints manager: 2.71 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: 2797 1.34 - 1.47: 2236 1.47 - 1.59: 3834 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 8955 Sorted by residual: bond pdb=" C ARG D 22 " pdb=" N PRO D 23 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.06e+01 bond pdb=" C TYR D 79 " pdb=" N PRO D 80 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.55e+00 bond pdb=" C LEU D 160 " pdb=" N PRO D 161 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.11e+00 bond pdb=" C VAL D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.333 1.362 -0.029 1.44e-02 4.82e+03 3.94e+00 bond pdb=" CA ARG D 59 " pdb=" CB ARG D 59 " ideal model delta sigma weight residual 1.541 1.560 -0.019 1.20e-02 6.94e+03 2.47e+00 ... (remaining 8950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11812 2.56 - 5.12: 277 5.12 - 7.68: 38 7.68 - 10.24: 9 10.24 - 12.80: 1 Bond angle restraints: 12137 Sorted by residual: angle pdb=" N ARG D 59 " pdb=" CA ARG D 59 " pdb=" CB ARG D 59 " ideal model delta sigma weight residual 114.17 108.97 5.20 1.14e+00 7.69e-01 2.08e+01 angle pdb=" CA LYS D 56 " pdb=" CB LYS D 56 " pdb=" CG LYS D 56 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" C GLN E 219 " pdb=" N HIS E 220 " pdb=" CA HIS E 220 " ideal model delta sigma weight residual 121.54 113.83 7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C LEU A 232 " pdb=" N VAL A 233 " pdb=" CA VAL A 233 " ideal model delta sigma weight residual 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" N ILE D 174 " pdb=" CA ILE D 174 " pdb=" C ILE D 174 " ideal model delta sigma weight residual 109.34 101.40 7.94 2.08e+00 2.31e-01 1.46e+01 ... (remaining 12132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 4941 22.36 - 44.72: 351 44.72 - 67.08: 16 67.08 - 89.44: 4 89.44 - 111.80: 2 Dihedral angle restraints: 5314 sinusoidal: 2072 harmonic: 3242 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -131.67 45.67 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1035 0.059 - 0.118: 268 0.118 - 0.177: 62 0.177 - 0.236: 7 0.236 - 0.294: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL D 198 " pdb=" CA VAL D 198 " pdb=" CG1 VAL D 198 " pdb=" CG2 VAL D 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1371 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 58 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C LEU D 58 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU D 58 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 59 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 198 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.28e+00 pdb=" N PRO D 199 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 JEV D 401 " 0.021 2.00e-02 2.50e+03 1.89e-02 8.96e+00 pdb=" C11 JEV D 401 " 0.019 2.00e-02 2.50e+03 pdb=" C12 JEV D 401 " 0.002 2.00e-02 2.50e+03 pdb=" C13 JEV D 401 " -0.002 2.00e-02 2.50e+03 pdb=" C14 JEV D 401 " 0.019 2.00e-02 2.50e+03 pdb=" C16 JEV D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C6 JEV D 401 " 0.010 2.00e-02 2.50e+03 pdb=" C8 JEV D 401 " -0.030 2.00e-02 2.50e+03 pdb=" C9 JEV D 401 " 0.002 2.00e-02 2.50e+03 pdb=" O1 JEV D 401 " -0.037 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1533 2.77 - 3.30: 7830 3.30 - 3.83: 14608 3.83 - 4.37: 17024 4.37 - 4.90: 29606 Nonbonded interactions: 70601 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 163 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 256 " pdb=" OG1 THR A 260 " model vdw 2.297 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.298 3.040 ... (remaining 70596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.006 0.060 8959 Z= 0.262 Angle : 0.963 12.803 12145 Z= 0.532 Chirality : 0.057 0.294 1374 Planarity : 0.007 0.076 1530 Dihedral : 14.282 111.800 3214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.90 % Rotamer: Outliers : 0.63 % Allowed : 8.67 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.08 (0.21), residues: 1098 helix: -2.93 (0.20), residues: 345 sheet: -2.22 (0.27), residues: 264 loop : -2.69 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.002 HIS E 35 PHE 0.024 0.003 PHE A 189 TYR 0.029 0.002 TYR E 178 ARG 0.005 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.13132 ( 381) hydrogen bonds : angle 7.20774 ( 1077) SS BOND : bond 0.01219 ( 4) SS BOND : angle 1.54790 ( 8) covalent geometry : bond 0.00556 ( 8955) covalent geometry : angle 0.96237 (12137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6553 (ttm) cc_final: 0.6179 (ttt) REVERT: A 29 LYS cc_start: 0.7616 (mppt) cc_final: 0.7035 (mmmt) REVERT: A 197 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7201 (mttm) REVERT: B 61 MET cc_start: 0.8709 (tmm) cc_final: 0.8360 (ppp) REVERT: B 217 MET cc_start: 0.6460 (ttp) cc_final: 0.5701 (tmm) REVERT: B 239 ASN cc_start: 0.7775 (m-40) cc_final: 0.7492 (t0) REVERT: B 271 CYS cc_start: 0.6295 (p) cc_final: 0.5984 (m) REVERT: B 280 LYS cc_start: 0.8129 (tttt) cc_final: 0.7836 (tptt) REVERT: E 64 VAL cc_start: 0.8215 (m) cc_final: 0.7812 (t) REVERT: E 87 ARG cc_start: 0.7091 (mpt90) cc_final: 0.6683 (mtp180) REVERT: E 93 MET cc_start: 0.7257 (tpp) cc_final: 0.6814 (tpp) REVERT: E 208 GLU cc_start: 0.7733 (tt0) cc_final: 0.7468 (mm-30) REVERT: E 222 GLU cc_start: 0.7706 (tt0) cc_final: 0.7425 (tt0) REVERT: E 232 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7643 (ttpp) REVERT: D 34 LEU cc_start: 0.7090 (tt) cc_final: 0.6633 (mt) REVERT: D 107 MET cc_start: 0.5796 (ttm) cc_final: 0.4935 (tmm) REVERT: D 116 PHE cc_start: 0.7878 (m-10) cc_final: 0.7632 (m-10) REVERT: D 126 TYR cc_start: 0.8098 (t80) cc_final: 0.7631 (t80) REVERT: D 131 HIS cc_start: 0.6741 (t70) cc_final: 0.6347 (t-170) REVERT: D 154 LEU cc_start: 0.6121 (tt) cc_final: 0.5920 (mt) REVERT: D 179 PHE cc_start: 0.6708 (t80) cc_final: 0.6352 (t80) REVERT: D 277 PHE cc_start: 0.5699 (t80) cc_final: 0.5478 (t80) REVERT: D 293 ILE cc_start: 0.7354 (mm) cc_final: 0.6975 (mm) outliers start: 6 outliers final: 0 residues processed: 193 average time/residue: 0.2368 time to fit residues: 61.7105 Evaluate side-chains 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 91 HIS B 142 HIS B 176 GLN B 293 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS D 255 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.203719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153279 restraints weight = 9455.118| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.72 r_work: 0.3486 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8959 Z= 0.183 Angle : 0.719 17.942 12145 Z= 0.377 Chirality : 0.045 0.218 1374 Planarity : 0.005 0.057 1530 Dihedral : 6.583 57.482 1232 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.62 % Rotamer: Outliers : 2.61 % Allowed : 14.63 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.20 (0.23), residues: 1098 helix: -1.72 (0.25), residues: 349 sheet: -1.91 (0.29), residues: 247 loop : -2.46 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 93 HIS 0.006 0.002 HIS B 91 PHE 0.022 0.002 PHE B 253 TYR 0.026 0.002 TYR E 178 ARG 0.004 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 381) hydrogen bonds : angle 5.81414 ( 1077) SS BOND : bond 0.02227 ( 4) SS BOND : angle 3.39516 ( 8) covalent geometry : bond 0.00411 ( 8955) covalent geometry : angle 0.71355 (12137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7645 (ttm) cc_final: 0.7305 (ttt) REVERT: A 29 LYS cc_start: 0.7909 (mppt) cc_final: 0.7538 (mmmt) REVERT: A 185 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7428 (m) REVERT: A 197 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7720 (mttm) REVERT: A 247 MET cc_start: 0.3749 (mmt) cc_final: 0.3484 (mmp) REVERT: A 349 LYS cc_start: 0.8560 (tttt) cc_final: 0.8141 (ttmm) REVERT: B 118 ASP cc_start: 0.8374 (p0) cc_final: 0.7972 (p0) REVERT: B 119 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9110 (m-40) REVERT: B 271 CYS cc_start: 0.6434 (p) cc_final: 0.5743 (m) REVERT: B 280 LYS cc_start: 0.8436 (tttt) cc_final: 0.8086 (tptt) REVERT: C 32 LYS cc_start: 0.7096 (mptt) cc_final: 0.6515 (ptpt) REVERT: E 18 ARG cc_start: 0.7525 (tpp80) cc_final: 0.7291 (tpp80) REVERT: E 19 LYS cc_start: 0.8210 (tttt) cc_final: 0.7870 (tttm) REVERT: E 62 ASP cc_start: 0.8339 (m-30) cc_final: 0.8014 (m-30) REVERT: E 74 ASP cc_start: 0.7895 (m-30) cc_final: 0.7459 (m-30) REVERT: E 87 ARG cc_start: 0.7556 (mpt90) cc_final: 0.7080 (mtp180) REVERT: E 93 MET cc_start: 0.7906 (tpp) cc_final: 0.7411 (tpp) REVERT: E 190 ARG cc_start: 0.6998 (ptt-90) cc_final: 0.6788 (ptt-90) REVERT: E 208 GLU cc_start: 0.7940 (tt0) cc_final: 0.7440 (mm-30) REVERT: E 210 GLU cc_start: 0.7075 (pp20) cc_final: 0.6634 (pp20) REVERT: E 232 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8301 (ttmt) REVERT: D 34 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6695 (mp) REVERT: D 86 MET cc_start: 0.7316 (ttt) cc_final: 0.7031 (tmm) REVERT: D 107 MET cc_start: 0.6045 (ttm) cc_final: 0.5391 (ttm) REVERT: D 131 HIS cc_start: 0.7142 (t70) cc_final: 0.6910 (t70) REVERT: D 147 TYR cc_start: 0.7083 (m-10) cc_final: 0.6092 (m-80) REVERT: D 251 TRP cc_start: 0.7463 (m100) cc_final: 0.6941 (m100) REVERT: D 293 ILE cc_start: 0.7338 (mm) cc_final: 0.6879 (mm) REVERT: D 303 ARG cc_start: 0.6297 (mtm180) cc_final: 0.5885 (mtm180) outliers start: 25 outliers final: 18 residues processed: 176 average time/residue: 0.2288 time to fit residues: 54.3979 Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 44 optimal weight: 0.0470 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.204662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.154996 restraints weight = 9555.028| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.76 r_work: 0.3496 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8959 Z= 0.157 Angle : 0.671 16.289 12145 Z= 0.350 Chirality : 0.044 0.201 1374 Planarity : 0.005 0.054 1530 Dihedral : 6.160 61.697 1232 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 3.87 % Allowed : 16.20 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.51 (0.24), residues: 1098 helix: -0.91 (0.27), residues: 339 sheet: -1.50 (0.30), residues: 261 loop : -2.24 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.002 PHE A 189 TYR 0.023 0.001 TYR E 178 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 381) hydrogen bonds : angle 5.51183 ( 1077) SS BOND : bond 0.01359 ( 4) SS BOND : angle 2.97095 ( 8) covalent geometry : bond 0.00357 ( 8955) covalent geometry : angle 0.66692 (12137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7697 (ttm) cc_final: 0.7327 (ttt) REVERT: A 185 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7559 (m) REVERT: A 197 LYS cc_start: 0.8404 (mtpt) cc_final: 0.7725 (mttm) REVERT: A 349 LYS cc_start: 0.8467 (tttt) cc_final: 0.8114 (ttmm) REVERT: B 118 ASP cc_start: 0.8210 (p0) cc_final: 0.7775 (t0) REVERT: B 130 GLU cc_start: 0.7882 (mp0) cc_final: 0.6940 (mp0) REVERT: B 280 LYS cc_start: 0.8635 (tttt) cc_final: 0.8227 (tptt) REVERT: E 74 ASP cc_start: 0.7545 (m-30) cc_final: 0.7186 (m-30) REVERT: E 87 ARG cc_start: 0.7470 (mpt90) cc_final: 0.6973 (mtp180) REVERT: E 93 MET cc_start: 0.7835 (tpp) cc_final: 0.7354 (tpp) REVERT: E 190 ARG cc_start: 0.7123 (ptt-90) cc_final: 0.6897 (ptt-90) REVERT: E 208 GLU cc_start: 0.7871 (tt0) cc_final: 0.7409 (mm-30) REVERT: E 210 GLU cc_start: 0.7056 (pp20) cc_final: 0.6747 (pp20) REVERT: E 232 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8201 (ttmm) REVERT: D 34 LEU cc_start: 0.7106 (tt) cc_final: 0.6662 (mp) REVERT: D 86 MET cc_start: 0.7456 (ttt) cc_final: 0.7082 (ttt) REVERT: D 107 MET cc_start: 0.5770 (ttm) cc_final: 0.5502 (ttm) REVERT: D 131 HIS cc_start: 0.7338 (t70) cc_final: 0.7075 (t70) REVERT: D 147 TYR cc_start: 0.7134 (m-10) cc_final: 0.5998 (m-80) REVERT: D 169 GLN cc_start: 0.7868 (pp30) cc_final: 0.7375 (pp30) REVERT: D 251 TRP cc_start: 0.7569 (m100) cc_final: 0.7346 (m100) REVERT: D 293 ILE cc_start: 0.7331 (mm) cc_final: 0.6873 (mm) REVERT: D 303 ARG cc_start: 0.6334 (mtm180) cc_final: 0.5894 (mtm180) REVERT: D 305 GLU cc_start: 0.5317 (tm-30) cc_final: 0.4964 (tt0) outliers start: 37 outliers final: 26 residues processed: 169 average time/residue: 0.2220 time to fit residues: 51.0310 Evaluate side-chains 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** 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 = 0.4313 r_free = 0.4313 target = 0.203570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153393 restraints weight = 9505.848| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.70 r_work: 0.3485 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8959 Z= 0.165 Angle : 0.677 17.726 12145 Z= 0.351 Chirality : 0.045 0.252 1374 Planarity : 0.004 0.049 1530 Dihedral : 6.072 62.919 1232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 4.08 % Allowed : 18.08 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.26 (0.24), residues: 1098 helix: -0.63 (0.28), residues: 342 sheet: -1.33 (0.30), residues: 263 loop : -2.17 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.005 0.001 HIS E 35 PHE 0.029 0.002 PHE A 191 TYR 0.024 0.001 TYR E 178 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 381) hydrogen bonds : angle 5.45247 ( 1077) SS BOND : bond 0.01409 ( 4) SS BOND : angle 3.27024 ( 8) covalent geometry : bond 0.00375 ( 8955) covalent geometry : angle 0.67152 (12137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7710 (ttm) cc_final: 0.7320 (ttt) REVERT: A 185 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7515 (m) REVERT: A 197 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7702 (mttm) REVERT: A 247 MET cc_start: 0.3795 (mmt) cc_final: 0.3362 (mmp) REVERT: A 266 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.4997 (mm) REVERT: A 349 LYS cc_start: 0.8603 (tttt) cc_final: 0.8212 (ttmm) REVERT: B 118 ASP cc_start: 0.8146 (p0) cc_final: 0.7764 (p0) REVERT: B 130 GLU cc_start: 0.7851 (mp0) cc_final: 0.6958 (mp0) REVERT: B 264 TYR cc_start: 0.8142 (m-80) cc_final: 0.7911 (m-80) REVERT: B 280 LYS cc_start: 0.8618 (tttt) cc_final: 0.8228 (tptt) REVERT: E 19 LYS cc_start: 0.8213 (tttt) cc_final: 0.7950 (tttm) REVERT: E 62 ASP cc_start: 0.8433 (m-30) cc_final: 0.8115 (m-30) REVERT: E 87 ARG cc_start: 0.7479 (mpt90) cc_final: 0.7003 (mtp180) REVERT: E 93 MET cc_start: 0.7761 (tpp) cc_final: 0.7242 (tpp) REVERT: E 208 GLU cc_start: 0.7866 (tt0) cc_final: 0.7379 (mm-30) REVERT: E 210 GLU cc_start: 0.7026 (pp20) cc_final: 0.6730 (pp20) REVERT: E 232 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8241 (ttmm) REVERT: D 34 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6557 (mp) REVERT: D 86 MET cc_start: 0.7491 (ttt) cc_final: 0.7131 (ttt) REVERT: D 107 MET cc_start: 0.5780 (ttm) cc_final: 0.5538 (ttm) REVERT: D 131 HIS cc_start: 0.7311 (t70) cc_final: 0.7025 (t70) REVERT: D 147 TYR cc_start: 0.7150 (m-10) cc_final: 0.6052 (m-80) REVERT: D 163 LEU cc_start: 0.7019 (mt) cc_final: 0.6714 (mt) REVERT: D 169 GLN cc_start: 0.7801 (pp30) cc_final: 0.7382 (pp30) REVERT: D 293 ILE cc_start: 0.7354 (mm) cc_final: 0.6895 (mm) REVERT: D 303 ARG cc_start: 0.6636 (mtm180) cc_final: 0.6123 (mtm180) REVERT: D 305 GLU cc_start: 0.5563 (tm-30) cc_final: 0.5162 (tt0) outliers start: 39 outliers final: 27 residues processed: 175 average time/residue: 0.1992 time to fit residues: 48.4336 Evaluate side-chains 170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** 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 = 0.4280 r_free = 0.4280 target = 0.199863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150474 restraints weight = 9525.688| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.76 r_work: 0.3438 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 8959 Z= 0.214 Angle : 0.702 12.551 12145 Z= 0.370 Chirality : 0.046 0.252 1374 Planarity : 0.005 0.050 1530 Dihedral : 6.281 65.697 1232 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.71 % Rotamer: Outliers : 4.18 % Allowed : 18.81 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.13 (0.24), residues: 1098 helix: -0.49 (0.28), residues: 341 sheet: -1.28 (0.30), residues: 252 loop : -2.11 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.006 0.002 HIS E 35 PHE 0.022 0.002 PHE B 253 TYR 0.027 0.002 TYR E 178 ARG 0.003 0.000 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 381) hydrogen bonds : angle 5.53731 ( 1077) SS BOND : bond 0.01375 ( 4) SS BOND : angle 2.55127 ( 8) covalent geometry : bond 0.00497 ( 8955) covalent geometry : angle 0.69915 (12137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7845 (ttm) cc_final: 0.7528 (ttt) REVERT: A 185 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7535 (m) REVERT: A 197 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7495 (mttm) REVERT: A 247 MET cc_start: 0.3870 (mmt) cc_final: 0.3617 (mmp) REVERT: A 266 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.4932 (mm) REVERT: A 349 LYS cc_start: 0.8475 (tttt) cc_final: 0.8100 (ttmm) REVERT: B 118 ASP cc_start: 0.8267 (p0) cc_final: 0.7973 (p0) REVERT: B 130 GLU cc_start: 0.7810 (mp0) cc_final: 0.6762 (mp0) REVERT: B 234 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: B 264 TYR cc_start: 0.8286 (m-80) cc_final: 0.7899 (m-80) REVERT: B 280 LYS cc_start: 0.8612 (tttt) cc_final: 0.8273 (tptt) REVERT: C 21 MET cc_start: 0.5893 (mmt) cc_final: 0.5657 (mmt) REVERT: C 48 ASP cc_start: 0.8226 (t0) cc_final: 0.7983 (t0) REVERT: E 19 LYS cc_start: 0.8319 (tttt) cc_final: 0.8030 (tttm) REVERT: E 87 ARG cc_start: 0.7544 (mpt90) cc_final: 0.7278 (mtp180) REVERT: E 93 MET cc_start: 0.7647 (tpp) cc_final: 0.7087 (tpp) REVERT: E 208 GLU cc_start: 0.7746 (tt0) cc_final: 0.6965 (mm-30) REVERT: E 210 GLU cc_start: 0.6852 (pp20) cc_final: 0.6621 (pp20) REVERT: E 232 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8240 (ttmm) REVERT: D 34 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6601 (mp) REVERT: D 86 MET cc_start: 0.7574 (ttt) cc_final: 0.7226 (ttt) REVERT: D 107 MET cc_start: 0.5896 (ttm) cc_final: 0.5477 (ttm) REVERT: D 131 HIS cc_start: 0.7281 (t70) cc_final: 0.6998 (t70) REVERT: D 169 GLN cc_start: 0.7618 (pp30) cc_final: 0.7355 (pp30) REVERT: D 305 GLU cc_start: 0.5362 (tm-30) cc_final: 0.4799 (tt0) outliers start: 40 outliers final: 28 residues processed: 183 average time/residue: 0.2133 time to fit residues: 54.6684 Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 104 optimal weight: 0.0000 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.201912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151864 restraints weight = 9401.469| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.76 r_work: 0.3411 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 8959 Z= 0.185 Angle : 0.673 12.192 12145 Z= 0.352 Chirality : 0.045 0.234 1374 Planarity : 0.004 0.047 1530 Dihedral : 6.083 65.642 1232 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 4.49 % Allowed : 19.64 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.97 (0.25), residues: 1098 helix: -0.26 (0.28), residues: 338 sheet: -1.16 (0.30), residues: 253 loop : -2.09 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.005 0.001 HIS E 35 PHE 0.027 0.002 PHE A 191 TYR 0.027 0.002 TYR E 178 ARG 0.006 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 381) hydrogen bonds : angle 5.38772 ( 1077) SS BOND : bond 0.01107 ( 4) SS BOND : angle 2.32384 ( 8) covalent geometry : bond 0.00429 ( 8955) covalent geometry : angle 0.67032 (12137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7842 (ttm) cc_final: 0.7524 (ttt) REVERT: A 185 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7777 (m) REVERT: A 197 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7613 (mttm) REVERT: A 247 MET cc_start: 0.4032 (mmt) cc_final: 0.3524 (mmp) REVERT: A 266 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5219 (mm) REVERT: A 349 LYS cc_start: 0.8391 (tttt) cc_final: 0.8105 (ttmm) REVERT: B 118 ASP cc_start: 0.8168 (p0) cc_final: 0.7870 (p0) REVERT: B 130 GLU cc_start: 0.7738 (mp0) cc_final: 0.6803 (mp0) REVERT: B 205 ASP cc_start: 0.7700 (p0) cc_final: 0.7452 (p0) REVERT: B 234 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: B 280 LYS cc_start: 0.8634 (tttt) cc_final: 0.8164 (tptt) REVERT: C 21 MET cc_start: 0.6040 (mmt) cc_final: 0.5801 (mmt) REVERT: E 74 ASP cc_start: 0.7612 (m-30) cc_final: 0.7347 (m-30) REVERT: E 87 ARG cc_start: 0.7577 (mpt90) cc_final: 0.7302 (mtp180) REVERT: E 93 MET cc_start: 0.7711 (tpp) cc_final: 0.7293 (tpp) REVERT: E 208 GLU cc_start: 0.7790 (tt0) cc_final: 0.7188 (mm-30) REVERT: E 232 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8380 (ttmm) REVERT: D 34 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6756 (mp) REVERT: D 107 MET cc_start: 0.6238 (ttm) cc_final: 0.5688 (ttm) REVERT: D 131 HIS cc_start: 0.7128 (t70) cc_final: 0.6873 (t70) REVERT: D 169 GLN cc_start: 0.7396 (pp30) cc_final: 0.7062 (pp30) REVERT: D 303 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6592 (mtm180) REVERT: D 305 GLU cc_start: 0.5365 (tm-30) cc_final: 0.4839 (tt0) outliers start: 43 outliers final: 31 residues processed: 184 average time/residue: 0.2082 time to fit residues: 52.9425 Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** 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 = 0.4315 r_free = 0.4315 target = 0.203655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153767 restraints weight = 9483.268| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.54 r_work: 0.3461 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8959 Z= 0.158 Angle : 0.672 15.718 12145 Z= 0.347 Chirality : 0.044 0.226 1374 Planarity : 0.004 0.044 1530 Dihedral : 5.899 64.891 1232 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 4.08 % Allowed : 20.69 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.71 (0.25), residues: 1098 helix: 0.09 (0.29), residues: 331 sheet: -1.02 (0.31), residues: 248 loop : -2.01 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 275 HIS 0.005 0.001 HIS E 35 PHE 0.027 0.002 PHE A 191 TYR 0.026 0.002 TYR E 178 ARG 0.011 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 381) hydrogen bonds : angle 5.33812 ( 1077) SS BOND : bond 0.01326 ( 4) SS BOND : angle 3.93119 ( 8) covalent geometry : bond 0.00364 ( 8955) covalent geometry : angle 0.66476 (12137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7723 (ttm) cc_final: 0.7395 (ttt) REVERT: A 197 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7433 (mttm) REVERT: A 247 MET cc_start: 0.4157 (mmt) cc_final: 0.3655 (mmp) REVERT: A 349 LYS cc_start: 0.8368 (tttt) cc_final: 0.8043 (ttmm) REVERT: B 118 ASP cc_start: 0.8154 (p0) cc_final: 0.7839 (p0) REVERT: B 130 GLU cc_start: 0.7662 (mp0) cc_final: 0.6659 (mp0) REVERT: B 205 ASP cc_start: 0.7420 (p0) cc_final: 0.7176 (p0) REVERT: B 234 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: B 280 LYS cc_start: 0.8626 (tttt) cc_final: 0.8051 (tptt) REVERT: C 21 MET cc_start: 0.6036 (mmt) cc_final: 0.5784 (mmt) REVERT: E 74 ASP cc_start: 0.7701 (m-30) cc_final: 0.7393 (m-30) REVERT: E 87 ARG cc_start: 0.7551 (mpt90) cc_final: 0.7217 (mtp180) REVERT: E 93 MET cc_start: 0.7570 (tpp) cc_final: 0.7095 (tpp) REVERT: E 208 GLU cc_start: 0.7743 (tt0) cc_final: 0.7169 (mm-30) REVERT: E 232 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8254 (ttmm) REVERT: D 34 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6583 (mp) REVERT: D 107 MET cc_start: 0.5933 (ttm) cc_final: 0.5313 (ttm) REVERT: D 131 HIS cc_start: 0.7111 (t70) cc_final: 0.6608 (t70) REVERT: D 134 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7957 (mppt) REVERT: D 169 GLN cc_start: 0.7300 (pp30) cc_final: 0.6912 (pp30) REVERT: D 208 LEU cc_start: 0.6885 (mt) cc_final: 0.5884 (mt) REVERT: D 303 ARG cc_start: 0.7012 (mtm180) cc_final: 0.6579 (mtm180) REVERT: D 305 GLU cc_start: 0.5251 (tm-30) cc_final: 0.4706 (tt0) outliers start: 39 outliers final: 30 residues processed: 178 average time/residue: 0.2003 time to fit residues: 49.3582 Evaluate side-chains 177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN E 130 GLN E 220 HIS D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.207180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158868 restraints weight = 9473.007| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.83 r_work: 0.3443 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8959 Z= 0.124 Angle : 0.639 15.132 12145 Z= 0.329 Chirality : 0.043 0.214 1374 Planarity : 0.004 0.042 1530 Dihedral : 5.570 63.529 1232 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 3.45 % Allowed : 21.11 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.46 (0.25), residues: 1098 helix: 0.23 (0.29), residues: 343 sheet: -0.80 (0.32), residues: 250 loop : -1.89 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 275 HIS 0.003 0.001 HIS A 213 PHE 0.024 0.002 PHE A 191 TYR 0.024 0.001 TYR E 178 ARG 0.009 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 381) hydrogen bonds : angle 5.13415 ( 1077) SS BOND : bond 0.01115 ( 4) SS BOND : angle 3.58343 ( 8) covalent geometry : bond 0.00283 ( 8955) covalent geometry : angle 0.63216 (12137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7684 (ttm) cc_final: 0.7348 (ttt) REVERT: A 197 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7422 (mttm) REVERT: A 247 MET cc_start: 0.4333 (mmt) cc_final: 0.3863 (mmp) REVERT: A 266 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5657 (mm) REVERT: A 349 LYS cc_start: 0.8214 (tttt) cc_final: 0.7988 (ttmm) REVERT: B 17 GLN cc_start: 0.3667 (OUTLIER) cc_final: 0.3414 (mp10) REVERT: B 118 ASP cc_start: 0.8023 (p0) cc_final: 0.7794 (t0) REVERT: B 130 GLU cc_start: 0.7863 (mp0) cc_final: 0.6928 (mp0) REVERT: B 205 ASP cc_start: 0.7370 (p0) cc_final: 0.7141 (p0) REVERT: B 234 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: B 280 LYS cc_start: 0.8617 (tttt) cc_final: 0.8327 (ttpp) REVERT: E 74 ASP cc_start: 0.7872 (m-30) cc_final: 0.7587 (m-30) REVERT: E 83 MET cc_start: 0.8618 (mtm) cc_final: 0.8386 (mtp) REVERT: E 93 MET cc_start: 0.7598 (tpp) cc_final: 0.7135 (tpp) REVERT: E 190 ARG cc_start: 0.7165 (ptt-90) cc_final: 0.6891 (ptt-90) REVERT: E 208 GLU cc_start: 0.8006 (tt0) cc_final: 0.7177 (mm-30) REVERT: E 232 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8221 (ttmm) REVERT: D 34 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6526 (mp) REVERT: D 107 MET cc_start: 0.5926 (ttm) cc_final: 0.5402 (ttm) REVERT: D 131 HIS cc_start: 0.7180 (t70) cc_final: 0.6717 (t70) REVERT: D 134 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7931 (mppt) REVERT: D 169 GLN cc_start: 0.7233 (pp30) cc_final: 0.6899 (pp30) REVERT: D 303 ARG cc_start: 0.6676 (mtm180) cc_final: 0.6297 (mtm180) REVERT: D 305 GLU cc_start: 0.5160 (tm-30) cc_final: 0.4668 (tt0) outliers start: 33 outliers final: 25 residues processed: 178 average time/residue: 0.2144 time to fit residues: 52.3814 Evaluate side-chains 172 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.202539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153573 restraints weight = 9569.340| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.05 r_work: 0.3434 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 8959 Z= 0.200 Angle : 0.705 13.503 12145 Z= 0.366 Chirality : 0.046 0.242 1374 Planarity : 0.004 0.044 1530 Dihedral : 5.866 66.051 1232 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.62 % Rotamer: Outliers : 3.66 % Allowed : 21.42 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.59 (0.25), residues: 1098 helix: 0.05 (0.28), residues: 349 sheet: -0.89 (0.31), residues: 248 loop : -1.92 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 275 HIS 0.006 0.001 HIS E 35 PHE 0.022 0.002 PHE A 191 TYR 0.027 0.002 TYR E 178 ARG 0.009 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 381) hydrogen bonds : angle 5.29819 ( 1077) SS BOND : bond 0.01361 ( 4) SS BOND : angle 3.87820 ( 8) covalent geometry : bond 0.00470 ( 8955) covalent geometry : angle 0.69838 (12137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7859 (ttm) cc_final: 0.7536 (ttt) REVERT: A 197 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7213 (mmtp) REVERT: A 247 MET cc_start: 0.4379 (mmt) cc_final: 0.3893 (mmp) REVERT: A 266 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5385 (mm) REVERT: A 349 LYS cc_start: 0.8084 (tttt) cc_final: 0.7880 (ttmm) REVERT: B 118 ASP cc_start: 0.8212 (p0) cc_final: 0.7921 (p0) REVERT: B 130 GLU cc_start: 0.7894 (mp0) cc_final: 0.6920 (mp0) REVERT: B 205 ASP cc_start: 0.7538 (p0) cc_final: 0.7312 (p0) REVERT: B 234 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: B 280 LYS cc_start: 0.8626 (tttt) cc_final: 0.8031 (tptt) REVERT: E 74 ASP cc_start: 0.7787 (m-30) cc_final: 0.7459 (m-30) REVERT: E 93 MET cc_start: 0.7643 (tpp) cc_final: 0.7182 (tpp) REVERT: E 190 ARG cc_start: 0.7170 (ptt-90) cc_final: 0.6967 (ptt-90) REVERT: E 208 GLU cc_start: 0.7997 (tt0) cc_final: 0.7079 (mm-30) REVERT: E 232 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8244 (ttmm) REVERT: D 34 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6522 (mp) REVERT: D 107 MET cc_start: 0.6587 (ttm) cc_final: 0.6037 (ttm) REVERT: D 131 HIS cc_start: 0.7176 (t70) cc_final: 0.6700 (t-90) REVERT: D 147 TYR cc_start: 0.6369 (m-80) cc_final: 0.6168 (m-80) REVERT: D 169 GLN cc_start: 0.7244 (pp30) cc_final: 0.6922 (pp30) REVERT: D 255 ASN cc_start: 0.7684 (m-40) cc_final: 0.7235 (m110) REVERT: D 303 ARG cc_start: 0.7096 (mtm180) cc_final: 0.6502 (mtm180) REVERT: D 305 GLU cc_start: 0.5538 (tm-30) cc_final: 0.4932 (tt0) outliers start: 35 outliers final: 26 residues processed: 176 average time/residue: 0.2164 time to fit residues: 51.9839 Evaluate side-chains 171 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 0.0670 chunk 90 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.205199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.146838 restraints weight = 9580.136| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.58 r_work: 0.3525 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8959 Z= 0.142 Angle : 0.696 17.708 12145 Z= 0.358 Chirality : 0.044 0.274 1374 Planarity : 0.004 0.054 1530 Dihedral : 5.649 64.261 1232 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 2.93 % Allowed : 22.47 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.39 (0.25), residues: 1098 helix: 0.22 (0.29), residues: 348 sheet: -0.77 (0.32), residues: 243 loop : -1.81 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 275 HIS 0.008 0.001 HIS B 225 PHE 0.023 0.002 PHE A 191 TYR 0.026 0.001 TYR E 178 ARG 0.014 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 381) hydrogen bonds : angle 5.19642 ( 1077) SS BOND : bond 0.01221 ( 4) SS BOND : angle 5.59197 ( 8) covalent geometry : bond 0.00321 ( 8955) covalent geometry : angle 0.68134 (12137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7896 (ttm) cc_final: 0.7569 (ttt) REVERT: A 197 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7137 (mmtp) REVERT: A 247 MET cc_start: 0.4345 (mmt) cc_final: 0.3912 (mmp) REVERT: A 266 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5558 (mm) REVERT: A 349 LYS cc_start: 0.8062 (tttt) cc_final: 0.7811 (ttmm) REVERT: B 205 ASP cc_start: 0.7510 (p0) cc_final: 0.7263 (p0) REVERT: B 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: B 280 LYS cc_start: 0.8617 (tttt) cc_final: 0.8330 (ttpp) REVERT: E 74 ASP cc_start: 0.7992 (m-30) cc_final: 0.7664 (m-30) REVERT: E 83 MET cc_start: 0.8593 (mtm) cc_final: 0.8223 (mtp) REVERT: E 93 MET cc_start: 0.7747 (tpp) cc_final: 0.7247 (tpp) REVERT: E 190 ARG cc_start: 0.6967 (ptt-90) cc_final: 0.6737 (ptt-90) REVERT: E 208 GLU cc_start: 0.8003 (tt0) cc_final: 0.6899 (mm-30) REVERT: E 232 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8048 (ttmm) REVERT: D 34 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6416 (mp) REVERT: D 107 MET cc_start: 0.6553 (ttm) cc_final: 0.6006 (ttm) REVERT: D 131 HIS cc_start: 0.7397 (t70) cc_final: 0.6749 (t70) REVERT: D 147 TYR cc_start: 0.6493 (m-80) cc_final: 0.6264 (m-80) REVERT: D 169 GLN cc_start: 0.7147 (pp30) cc_final: 0.6856 (pp30) REVERT: D 255 ASN cc_start: 0.7702 (m-40) cc_final: 0.7222 (m110) REVERT: D 303 ARG cc_start: 0.7038 (mtm180) cc_final: 0.6443 (mtm180) REVERT: D 305 GLU cc_start: 0.5164 (tm-30) cc_final: 0.4650 (tt0) outliers start: 28 outliers final: 23 residues processed: 170 average time/residue: 0.2193 time to fit residues: 50.8568 Evaluate side-chains 168 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS D 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.206140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156835 restraints weight = 9542.633| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.47 r_work: 0.3538 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8959 Z= 0.137 Angle : 0.688 16.764 12145 Z= 0.355 Chirality : 0.044 0.279 1374 Planarity : 0.004 0.065 1530 Dihedral : 5.585 64.051 1232 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 3.13 % Allowed : 22.36 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.24 (0.26), residues: 1098 helix: 0.35 (0.29), residues: 349 sheet: -0.50 (0.32), residues: 253 loop : -1.86 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 275 HIS 0.006 0.001 HIS E 220 PHE 0.022 0.002 PHE A 191 TYR 0.026 0.001 TYR E 178 ARG 0.014 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 381) hydrogen bonds : angle 5.14565 ( 1077) SS BOND : bond 0.01193 ( 4) SS BOND : angle 5.56720 ( 8) covalent geometry : bond 0.00310 ( 8955) covalent geometry : angle 0.67323 (12137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.47 seconds wall clock time: 85 minutes 33.91 seconds (5133.91 seconds total)