Starting phenix.real_space_refine on Sat Dec 28 00:23:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezk_31388/12_2024/7ezk_31388.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezk_31388/12_2024/7ezk_31388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ezk_31388/12_2024/7ezk_31388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezk_31388/12_2024/7ezk_31388.map" model { file = "/net/cci-nas-00/data/ceres_data/7ezk_31388/12_2024/7ezk_31388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezk_31388/12_2024/7ezk_31388.cif" } resolution = 3.1 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= 0.002 sd= 0.033 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 57 5.16 5 C 4584 2.51 5 N 1242 2.21 5 O 1313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1871 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2298 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 388 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.57, per 1000 atoms: 0.64 Number of scatterers: 7196 At special positions: 0 Unit cell: (102.41, 113.905, 101.365, 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 57 16.00 O 1313 8.00 N 1242 7.00 C 4584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 49.0% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.726A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.997A pdb=" N GLN A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 229 through 246 removed outlier: 3.974A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.947A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.651A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 removed outlier: 4.223A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 removed outlier: 5.314A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.566A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 69 removed outlier: 4.320A pdb=" N VAL D 43 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 95 Processing helix chain 'D' and resid 95 through 105 Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 110 through 145 Processing helix chain 'D' and resid 145 through 150 removed outlier: 4.279A pdb=" N ARG D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 154 through 173 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 202 through 218 Processing helix chain 'D' and resid 218 through 246 Processing helix chain 'D' and resid 302 through 339 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 349 through 371 removed outlier: 4.281A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 374 through 382 removed outlier: 4.503A pdb=" N GLY D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 4.049A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.339A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.703A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.718A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.407A 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: 7.012A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.783A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.922A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AB1, first strand: chain 'D' and resid 184 through 186 400 hydrogen bonds defined for protein. 1152 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: 2.17 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1832 1.33 - 1.46: 2104 1.46 - 1.60: 3323 1.60 - 1.73: 1 1.73 - 1.86: 84 Bond restraints: 7344 Sorted by residual: bond pdb=" O3 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.458 1.630 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.567 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O2 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.461 1.411 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" CZ ARG A 347 " pdb=" NH2 ARG A 347 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.21e+00 bond pdb=" CZ ARG A 31 " pdb=" NH1 ARG A 31 " ideal model delta sigma weight residual 1.323 1.354 -0.031 1.40e-02 5.10e+03 4.85e+00 ... (remaining 7339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 9672 2.41 - 4.81: 264 4.81 - 7.22: 21 7.22 - 9.62: 3 9.62 - 12.03: 2 Bond angle restraints: 9962 Sorted by residual: angle pdb=" O2 TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 115.38 103.35 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" OH TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 100.21 110.88 -10.67 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N ARG D 310 " pdb=" CA ARG D 310 " pdb=" C ARG D 310 " ideal model delta sigma weight residual 111.36 107.77 3.59 1.09e+00 8.42e-01 1.08e+01 angle pdb=" CZ TYS P 2 " pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 116.88 126.28 -9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " pdb=" NH1 ARG B 48 " ideal model delta sigma weight residual 121.50 118.68 2.82 1.00e+00 1.00e+00 7.93e+00 ... (remaining 9957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4031 17.82 - 35.64: 282 35.64 - 53.46: 41 53.46 - 71.28: 13 71.28 - 89.10: 7 Dihedral angle restraints: 4374 sinusoidal: 1681 harmonic: 2693 Sorted by residual: dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N VAL A 218 " pdb=" CA VAL A 218 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 4371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 698 0.053 - 0.105: 351 0.105 - 0.157: 81 0.157 - 0.210: 8 0.210 - 0.262: 4 Chirality restraints: 1142 Sorted by residual: chirality pdb=" CG LEU D 214 " pdb=" CB LEU D 214 " pdb=" CD1 LEU D 214 " pdb=" CD2 LEU D 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 151 " pdb=" CA VAL D 151 " pdb=" CG1 VAL D 151 " pdb=" CG2 VAL D 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1139 not shown) Planarity restraints: 1261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " 0.064 9.50e-02 1.11e+02 4.95e-02 2.07e+01 pdb=" NE ARG A 300 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " 0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C PRO D 367 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO D 367 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE D 368 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 214 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU D 214 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 214 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 215 " -0.022 2.00e-02 2.50e+03 ... (remaining 1258 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 689 2.74 - 3.28: 7507 3.28 - 3.82: 12112 3.82 - 4.36: 14972 4.36 - 4.90: 25331 Nonbonded interactions: 60611 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.286 3.040 nonbonded pdb=" NZ LYS D 115 " pdb=" O PRO D 177 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG A 205 " pdb=" OE1 GLU A 207 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG D 197 " pdb=" O1 TYS P 2 " model vdw 2.337 3.120 ... (remaining 60606 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.011 0.172 7344 Z= 0.693 Angle : 1.037 12.028 9962 Z= 0.616 Chirality : 0.061 0.262 1142 Planarity : 0.010 0.082 1261 Dihedral : 13.268 89.095 2619 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.26 % Allowed : 2.34 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.27), residues: 905 helix: -0.92 (0.22), residues: 399 sheet: 0.04 (0.38), residues: 191 loop : -0.47 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP B 99 HIS 0.020 0.007 HIS A 354 PHE 0.033 0.006 PHE G 61 TYR 0.028 0.008 TYR D 229 ARG 0.078 0.010 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.838 Fit side-chains REVERT: A 20 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6164 (mt-10) REVERT: A 216 ASN cc_start: 0.8316 (t0) cc_final: 0.8111 (t0) REVERT: A 223 PHE cc_start: 0.8172 (t80) cc_final: 0.7865 (t80) REVERT: A 276 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6866 (mt-10) REVERT: A 348 ASP cc_start: 0.7331 (t70) cc_final: 0.6992 (t0) REVERT: B 59 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: B 76 ASP cc_start: 0.6661 (t70) cc_final: 0.6347 (t0) REVERT: B 145 TYR cc_start: 0.8301 (p90) cc_final: 0.7667 (p90) REVERT: B 147 SER cc_start: 0.8402 (t) cc_final: 0.8053 (p) REVERT: B 149 CYS cc_start: 0.7155 (p) cc_final: 0.6674 (p) REVERT: B 150 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7427 (mmt-90) REVERT: B 188 MET cc_start: 0.7168 (tpt) cc_final: 0.6900 (mmm) REVERT: B 189 SER cc_start: 0.8346 (p) cc_final: 0.8026 (t) REVERT: B 191 SER cc_start: 0.8118 (m) cc_final: 0.7915 (p) REVERT: B 201 SER cc_start: 0.8254 (m) cc_final: 0.7588 (p) REVERT: B 273 ILE cc_start: 0.7793 (mt) cc_final: 0.7363 (mt) REVERT: B 277 SER cc_start: 0.8177 (t) cc_final: 0.7701 (m) REVERT: B 295 ASN cc_start: 0.7992 (m-40) cc_final: 0.7720 (m110) REVERT: B 325 MET cc_start: 0.6838 (tpp) cc_final: 0.6452 (tpp) REVERT: B 333 ASP cc_start: 0.6664 (m-30) cc_final: 0.6419 (m-30) REVERT: D 56 VAL cc_start: 0.6996 (t) cc_final: 0.6674 (m) REVERT: D 86 SER cc_start: 0.8548 (t) cc_final: 0.8144 (p) REVERT: D 117 THR cc_start: 0.7240 (m) cc_final: 0.6852 (p) REVERT: D 382 MET cc_start: 0.5512 (mpp) cc_final: 0.5130 (mpp) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.2027 time to fit residues: 59.6962 Evaluate side-chains 196 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN D 131 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7344 Z= 0.230 Angle : 0.576 5.712 9962 Z= 0.308 Chirality : 0.043 0.144 1142 Planarity : 0.004 0.056 1261 Dihedral : 5.907 49.008 998 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.95 % Allowed : 10.92 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 905 helix: 0.99 (0.26), residues: 397 sheet: -0.30 (0.36), residues: 196 loop : 0.21 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS A 324 PHE 0.013 0.001 PHE A 189 TYR 0.011 0.001 TYR A 325 ARG 0.006 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6181 (mt-10) REVERT: A 27 LYS cc_start: 0.8034 (tttt) cc_final: 0.7759 (tttm) REVERT: A 216 ASN cc_start: 0.8263 (t0) cc_final: 0.8023 (t0) REVERT: A 276 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 359 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6176 (mt-10) REVERT: B 59 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: B 68 ARG cc_start: 0.7495 (ttt90) cc_final: 0.7224 (ttt90) REVERT: B 145 TYR cc_start: 0.8359 (p90) cc_final: 0.7495 (p90) REVERT: B 147 SER cc_start: 0.8292 (t) cc_final: 0.7983 (t) REVERT: B 163 ASP cc_start: 0.7156 (p0) cc_final: 0.6787 (p0) REVERT: B 181 THR cc_start: 0.8088 (p) cc_final: 0.7691 (m) REVERT: B 188 MET cc_start: 0.6983 (tpt) cc_final: 0.6494 (mmm) REVERT: B 189 SER cc_start: 0.8330 (p) cc_final: 0.8019 (t) REVERT: B 201 SER cc_start: 0.8265 (m) cc_final: 0.7809 (p) REVERT: B 214 ARG cc_start: 0.7108 (mpt90) cc_final: 0.6665 (mpt180) REVERT: B 233 CYS cc_start: 0.7529 (t) cc_final: 0.7252 (t) REVERT: B 283 ARG cc_start: 0.8153 (tpt-90) cc_final: 0.7904 (tpt-90) REVERT: B 316 SER cc_start: 0.7646 (t) cc_final: 0.7372 (p) REVERT: B 325 MET cc_start: 0.6972 (tpp) cc_final: 0.6619 (tpp) REVERT: B 333 ASP cc_start: 0.6597 (m-30) cc_final: 0.6267 (m-30) REVERT: D 56 VAL cc_start: 0.7051 (t) cc_final: 0.6783 (m) REVERT: D 80 LEU cc_start: 0.7567 (mt) cc_final: 0.7259 (mp) REVERT: D 86 SER cc_start: 0.8649 (t) cc_final: 0.8402 (p) REVERT: D 104 LEU cc_start: 0.7906 (mt) cc_final: 0.7670 (mt) REVERT: D 121 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6992 (mtt) REVERT: D 182 LEU cc_start: 0.7964 (tp) cc_final: 0.7696 (tt) REVERT: D 195 MET cc_start: 0.7066 (ptp) cc_final: 0.6351 (mtm) outliers start: 15 outliers final: 8 residues processed: 216 average time/residue: 0.2052 time to fit residues: 59.0340 Evaluate side-chains 222 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7344 Z= 0.255 Angle : 0.562 6.322 9962 Z= 0.297 Chirality : 0.044 0.138 1142 Planarity : 0.005 0.054 1261 Dihedral : 5.521 49.366 998 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.99 % Allowed : 12.74 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 905 helix: 1.40 (0.26), residues: 391 sheet: -0.52 (0.35), residues: 201 loop : 0.35 (0.40), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.004 0.001 HIS A 324 PHE 0.016 0.001 PHE A 189 TYR 0.013 0.001 TYR D 176 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6330 (mt-10) REVERT: A 27 LYS cc_start: 0.8050 (tttt) cc_final: 0.7798 (tttp) REVERT: A 186 GLU cc_start: 0.6680 (tt0) cc_final: 0.6438 (tt0) REVERT: A 237 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 241 LYS cc_start: 0.7578 (ttmm) cc_final: 0.7352 (ttmm) REVERT: A 276 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6800 (mt-10) REVERT: A 309 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.7246 (ttp-170) REVERT: A 311 GLU cc_start: 0.6055 (mm-30) cc_final: 0.5442 (mm-30) REVERT: B 59 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: B 68 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7388 (ttt90) REVERT: B 83 ASP cc_start: 0.7813 (t0) cc_final: 0.7189 (t0) REVERT: B 145 TYR cc_start: 0.8394 (p90) cc_final: 0.7466 (p90) REVERT: B 147 SER cc_start: 0.8258 (t) cc_final: 0.7892 (t) REVERT: B 188 MET cc_start: 0.6999 (tpt) cc_final: 0.6641 (mmm) REVERT: B 189 SER cc_start: 0.8267 (p) cc_final: 0.8018 (p) REVERT: B 196 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 201 SER cc_start: 0.8310 (m) cc_final: 0.8026 (p) REVERT: B 214 ARG cc_start: 0.7290 (mpt90) cc_final: 0.6717 (mpt180) REVERT: B 219 ARG cc_start: 0.6942 (mmt180) cc_final: 0.6519 (mmt-90) REVERT: B 233 CYS cc_start: 0.7673 (t) cc_final: 0.7357 (t) REVERT: B 277 SER cc_start: 0.8127 (t) cc_final: 0.7589 (m) REVERT: B 304 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7314 (ttm170) REVERT: B 325 MET cc_start: 0.6930 (tpp) cc_final: 0.6593 (tpp) REVERT: D 56 VAL cc_start: 0.7263 (t) cc_final: 0.6972 (m) REVERT: D 98 ASN cc_start: 0.8140 (m-40) cc_final: 0.7642 (m110) REVERT: D 104 LEU cc_start: 0.7930 (mt) cc_final: 0.7670 (mt) REVERT: D 121 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7116 (mtm) REVERT: D 123 THR cc_start: 0.7852 (m) cc_final: 0.7648 (p) REVERT: D 136 SER cc_start: 0.8013 (t) cc_final: 0.7418 (p) REVERT: D 195 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6400 (mtm) outliers start: 23 outliers final: 14 residues processed: 232 average time/residue: 0.2368 time to fit residues: 69.5514 Evaluate side-chains 232 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7344 Z= 0.255 Angle : 0.555 7.681 9962 Z= 0.290 Chirality : 0.044 0.135 1142 Planarity : 0.005 0.055 1261 Dihedral : 5.315 48.510 998 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.16 % Allowed : 14.56 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 905 helix: 1.55 (0.27), residues: 392 sheet: -0.59 (0.35), residues: 197 loop : 0.25 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.004 0.001 HIS A 324 PHE 0.017 0.001 PHE A 189 TYR 0.012 0.001 TYR D 176 ARG 0.007 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7421 (mmtt) cc_final: 0.7064 (mmtt) REVERT: A 20 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6236 (mt-10) REVERT: A 186 GLU cc_start: 0.6727 (tt0) cc_final: 0.6496 (tt0) REVERT: A 267 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: A 276 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6837 (mt-10) REVERT: B 68 ARG cc_start: 0.7796 (ttt90) cc_final: 0.7405 (ttt90) REVERT: B 147 SER cc_start: 0.8279 (t) cc_final: 0.7811 (p) REVERT: B 189 SER cc_start: 0.8256 (p) cc_final: 0.8000 (p) REVERT: B 196 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7772 (m) REVERT: B 201 SER cc_start: 0.8332 (m) cc_final: 0.8098 (p) REVERT: B 214 ARG cc_start: 0.7235 (mpt90) cc_final: 0.6601 (mpt180) REVERT: B 219 ARG cc_start: 0.6932 (mmt180) cc_final: 0.6497 (mmt-90) REVERT: B 233 CYS cc_start: 0.7792 (t) cc_final: 0.7416 (t) REVERT: B 277 SER cc_start: 0.8116 (t) cc_final: 0.7523 (m) REVERT: B 295 ASN cc_start: 0.8149 (m-40) cc_final: 0.7843 (m-40) REVERT: B 304 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7411 (ttm170) REVERT: B 312 ASP cc_start: 0.6455 (t0) cc_final: 0.6070 (t70) REVERT: B 322 ASP cc_start: 0.6141 (t0) cc_final: 0.5919 (t0) REVERT: B 325 MET cc_start: 0.6902 (tpp) cc_final: 0.6580 (tpp) REVERT: D 56 VAL cc_start: 0.7301 (t) cc_final: 0.6965 (m) REVERT: D 98 ASN cc_start: 0.8228 (m-40) cc_final: 0.7761 (m110) REVERT: D 121 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7060 (mtm) REVERT: D 136 SER cc_start: 0.8009 (t) cc_final: 0.7369 (p) REVERT: D 137 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7501 (mt) REVERT: D 139 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7731 (mtt-85) REVERT: D 195 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6334 (mtm) REVERT: D 321 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6686 (tp) outliers start: 32 outliers final: 17 residues processed: 232 average time/residue: 0.2463 time to fit residues: 72.4082 Evaluate side-chains 233 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7344 Z= 0.225 Angle : 0.556 8.186 9962 Z= 0.285 Chirality : 0.043 0.133 1142 Planarity : 0.004 0.060 1261 Dihedral : 4.905 30.764 996 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.99 % Allowed : 17.17 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 905 helix: 1.63 (0.27), residues: 390 sheet: -0.73 (0.35), residues: 189 loop : 0.16 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.016 0.001 PHE A 189 TYR 0.011 0.001 TYR B 289 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7008 (mmtt) REVERT: A 20 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6277 (mt-10) REVERT: A 26 ASP cc_start: 0.6769 (m-30) cc_final: 0.6347 (m-30) REVERT: A 186 GLU cc_start: 0.6720 (tt0) cc_final: 0.6490 (tt0) REVERT: A 276 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6809 (mt-10) REVERT: B 68 ARG cc_start: 0.7735 (ttt90) cc_final: 0.7352 (ttt90) REVERT: B 147 SER cc_start: 0.8256 (t) cc_final: 0.7850 (p) REVERT: B 189 SER cc_start: 0.8181 (p) cc_final: 0.7910 (p) REVERT: B 196 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7761 (m) REVERT: B 214 ARG cc_start: 0.7309 (mpt90) cc_final: 0.6679 (mpt180) REVERT: B 219 ARG cc_start: 0.6908 (mmt180) cc_final: 0.6527 (mmt180) REVERT: B 233 CYS cc_start: 0.7812 (t) cc_final: 0.7421 (t) REVERT: B 277 SER cc_start: 0.8077 (t) cc_final: 0.7559 (m) REVERT: B 304 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7520 (ttm170) REVERT: B 322 ASP cc_start: 0.6265 (t0) cc_final: 0.6013 (t0) REVERT: B 325 MET cc_start: 0.6869 (tpp) cc_final: 0.6572 (tpp) REVERT: D 56 VAL cc_start: 0.7274 (t) cc_final: 0.6953 (m) REVERT: D 61 LEU cc_start: 0.7415 (mp) cc_final: 0.7155 (mt) REVERT: D 72 MET cc_start: 0.6414 (ttm) cc_final: 0.6146 (ttm) REVERT: D 121 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7070 (mtt) REVERT: D 136 SER cc_start: 0.8010 (t) cc_final: 0.7754 (t) REVERT: D 137 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7525 (mt) REVERT: D 139 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7717 (mtt180) REVERT: D 195 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6710 (mtm) outliers start: 23 outliers final: 13 residues processed: 224 average time/residue: 0.2457 time to fit residues: 69.6938 Evaluate side-chains 231 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain P residue 3 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7344 Z= 0.245 Angle : 0.553 7.981 9962 Z= 0.285 Chirality : 0.043 0.134 1142 Planarity : 0.004 0.057 1261 Dihedral : 4.870 30.075 996 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.25 % Allowed : 17.69 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 905 helix: 1.70 (0.27), residues: 390 sheet: -0.76 (0.36), residues: 185 loop : 0.28 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.017 0.002 PHE A 189 TYR 0.009 0.001 TYR D 176 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7164 (mmtt) REVERT: A 20 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6318 (mt-10) REVERT: A 26 ASP cc_start: 0.6772 (m-30) cc_final: 0.6341 (m-30) REVERT: A 186 GLU cc_start: 0.6728 (tt0) cc_final: 0.6498 (tt0) REVERT: B 59 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: B 68 ARG cc_start: 0.7766 (ttt90) cc_final: 0.7335 (ttt90) REVERT: B 101 MET cc_start: 0.7863 (mtp) cc_final: 0.7623 (mtp) REVERT: B 147 SER cc_start: 0.8278 (t) cc_final: 0.7858 (p) REVERT: B 189 SER cc_start: 0.8174 (p) cc_final: 0.7880 (p) REVERT: B 196 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7762 (m) REVERT: B 214 ARG cc_start: 0.7352 (mpt90) cc_final: 0.6718 (mpt180) REVERT: B 219 ARG cc_start: 0.6916 (mmt180) cc_final: 0.6456 (mmt-90) REVERT: B 233 CYS cc_start: 0.7831 (t) cc_final: 0.7443 (t) REVERT: B 277 SER cc_start: 0.8098 (t) cc_final: 0.7569 (m) REVERT: B 304 ARG cc_start: 0.7819 (ttm170) cc_final: 0.7536 (ttm170) REVERT: B 322 ASP cc_start: 0.6383 (t0) cc_final: 0.6127 (t0) REVERT: B 325 MET cc_start: 0.6842 (tpp) cc_final: 0.6598 (tpp) REVERT: D 56 VAL cc_start: 0.7340 (t) cc_final: 0.6921 (m) REVERT: D 72 MET cc_start: 0.6416 (ttm) cc_final: 0.6198 (ttm) REVERT: D 114 CYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5520 (t) REVERT: D 121 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7038 (mtm) REVERT: D 136 SER cc_start: 0.7997 (t) cc_final: 0.7736 (t) REVERT: D 137 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7602 (mt) REVERT: D 195 MET cc_start: 0.7080 (ptp) cc_final: 0.6837 (ptm) REVERT: D 321 LEU cc_start: 0.7056 (tt) cc_final: 0.6852 (tp) outliers start: 25 outliers final: 15 residues processed: 219 average time/residue: 0.2224 time to fit residues: 62.8682 Evaluate side-chains 230 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain P residue 3 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7344 Z= 0.218 Angle : 0.559 8.665 9962 Z= 0.284 Chirality : 0.043 0.137 1142 Planarity : 0.004 0.056 1261 Dihedral : 4.767 29.284 996 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.60 % Allowed : 19.51 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 905 helix: 1.77 (0.27), residues: 390 sheet: -0.79 (0.36), residues: 185 loop : 0.24 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 329 PHE 0.015 0.001 PHE A 189 TYR 0.009 0.001 TYR B 289 ARG 0.009 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7190 (mmtt) REVERT: A 20 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6319 (mt-10) REVERT: A 26 ASP cc_start: 0.6753 (m-30) cc_final: 0.6323 (m-30) REVERT: A 186 GLU cc_start: 0.6724 (tt0) cc_final: 0.6489 (tt0) REVERT: A 257 PHE cc_start: 0.7955 (m-10) cc_final: 0.7567 (m-80) REVERT: A 329 HIS cc_start: 0.8114 (m170) cc_final: 0.7707 (m170) REVERT: B 68 ARG cc_start: 0.7728 (ttt90) cc_final: 0.7263 (ttt90) REVERT: B 83 ASP cc_start: 0.7613 (t0) cc_final: 0.7000 (t70) REVERT: B 101 MET cc_start: 0.7862 (mtp) cc_final: 0.7580 (mtp) REVERT: B 139 LEU cc_start: 0.8508 (mt) cc_final: 0.8291 (mt) REVERT: B 189 SER cc_start: 0.8216 (p) cc_final: 0.7898 (p) REVERT: B 196 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7726 (m) REVERT: B 214 ARG cc_start: 0.7418 (mpt90) cc_final: 0.6756 (mpt180) REVERT: B 219 ARG cc_start: 0.6906 (mmt180) cc_final: 0.6447 (mmt-90) REVERT: B 230 ASN cc_start: 0.7389 (t0) cc_final: 0.7099 (m-40) REVERT: B 233 CYS cc_start: 0.7825 (t) cc_final: 0.7465 (t) REVERT: B 277 SER cc_start: 0.8168 (t) cc_final: 0.7577 (m) REVERT: B 304 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7544 (ttm170) REVERT: B 322 ASP cc_start: 0.6451 (t0) cc_final: 0.6195 (t0) REVERT: B 325 MET cc_start: 0.6853 (tpp) cc_final: 0.6545 (tpp) REVERT: D 72 MET cc_start: 0.6416 (ttm) cc_final: 0.6206 (ttm) REVERT: D 98 ASN cc_start: 0.8202 (m-40) cc_final: 0.7760 (m110) REVERT: D 115 LYS cc_start: 0.8057 (mttm) cc_final: 0.7824 (mttm) REVERT: D 121 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7043 (mtm) REVERT: D 136 SER cc_start: 0.8025 (t) cc_final: 0.7751 (t) REVERT: D 137 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (mt) REVERT: D 195 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6719 (ptm) REVERT: D 309 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7533 (mmmm) REVERT: D 321 LEU cc_start: 0.7073 (tt) cc_final: 0.6866 (tp) outliers start: 20 outliers final: 14 residues processed: 223 average time/residue: 0.2542 time to fit residues: 72.7233 Evaluate side-chains 228 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7344 Z= 0.270 Angle : 0.580 8.909 9962 Z= 0.297 Chirality : 0.044 0.143 1142 Planarity : 0.005 0.055 1261 Dihedral : 4.830 29.438 996 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.77 % Allowed : 19.51 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 905 helix: 1.76 (0.27), residues: 390 sheet: -0.82 (0.36), residues: 185 loop : 0.16 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 324 PHE 0.017 0.002 PHE A 189 TYR 0.011 0.001 TYR D 176 ARG 0.010 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7396 (mmtt) cc_final: 0.7018 (mmtt) REVERT: A 20 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6316 (mt-10) REVERT: A 186 GLU cc_start: 0.6686 (tt0) cc_final: 0.6458 (tt0) REVERT: A 313 LEU cc_start: 0.7582 (mm) cc_final: 0.7295 (mp) REVERT: A 314 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7399 (ttm110) REVERT: A 329 HIS cc_start: 0.8154 (m170) cc_final: 0.7771 (m170) REVERT: A 335 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: A 359 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6204 (mt-10) REVERT: B 59 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: B 68 ARG cc_start: 0.7775 (ttt90) cc_final: 0.7357 (ttt90) REVERT: B 101 MET cc_start: 0.7871 (mtp) cc_final: 0.7642 (mtp) REVERT: B 139 LEU cc_start: 0.8533 (mt) cc_final: 0.8313 (mt) REVERT: B 147 SER cc_start: 0.8293 (t) cc_final: 0.7800 (p) REVERT: B 189 SER cc_start: 0.8198 (p) cc_final: 0.7875 (p) REVERT: B 196 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 214 ARG cc_start: 0.7425 (mpt90) cc_final: 0.6871 (mpt180) REVERT: B 219 ARG cc_start: 0.6911 (mmt180) cc_final: 0.6484 (mmt180) REVERT: B 233 CYS cc_start: 0.7831 (t) cc_final: 0.7463 (t) REVERT: B 277 SER cc_start: 0.8200 (t) cc_final: 0.7620 (m) REVERT: B 304 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7559 (ttm170) REVERT: B 322 ASP cc_start: 0.6621 (t0) cc_final: 0.6350 (t0) REVERT: B 325 MET cc_start: 0.6845 (tpp) cc_final: 0.6552 (tpp) REVERT: D 72 MET cc_start: 0.6439 (ttm) cc_final: 0.6220 (ttm) REVERT: D 115 LYS cc_start: 0.7957 (mttm) cc_final: 0.7561 (mttm) REVERT: D 121 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7079 (mtm) REVERT: D 136 SER cc_start: 0.8091 (t) cc_final: 0.7785 (t) REVERT: D 309 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7630 (mmmm) outliers start: 29 outliers final: 16 residues processed: 230 average time/residue: 0.2489 time to fit residues: 72.9042 Evaluate side-chains 242 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain P residue 3 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 0.0070 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7344 Z= 0.200 Angle : 0.566 9.039 9962 Z= 0.288 Chirality : 0.043 0.182 1142 Planarity : 0.004 0.052 1261 Dihedral : 4.690 27.613 996 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.99 % Allowed : 19.90 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 905 helix: 1.85 (0.27), residues: 390 sheet: -0.80 (0.36), residues: 185 loop : 0.12 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS B 183 PHE 0.023 0.001 PHE D 198 TYR 0.009 0.001 TYR B 289 ARG 0.010 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7195 (mmtt) REVERT: A 20 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6331 (mt-10) REVERT: A 26 ASP cc_start: 0.6737 (m-30) cc_final: 0.6302 (m-30) REVERT: A 186 GLU cc_start: 0.6684 (tt0) cc_final: 0.6439 (tt0) REVERT: A 329 HIS cc_start: 0.8105 (m170) cc_final: 0.7732 (m170) REVERT: A 359 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6210 (mt-10) REVERT: B 68 ARG cc_start: 0.7692 (ttt90) cc_final: 0.7250 (ttt90) REVERT: B 83 ASP cc_start: 0.7611 (t0) cc_final: 0.7015 (t0) REVERT: B 101 MET cc_start: 0.7825 (mtp) cc_final: 0.7618 (mtp) REVERT: B 139 LEU cc_start: 0.8510 (mt) cc_final: 0.8307 (mt) REVERT: B 189 SER cc_start: 0.8272 (p) cc_final: 0.7944 (p) REVERT: B 214 ARG cc_start: 0.7462 (mpt90) cc_final: 0.6878 (mpt180) REVERT: B 219 ARG cc_start: 0.6882 (mmt180) cc_final: 0.6463 (mmt180) REVERT: B 230 ASN cc_start: 0.7511 (m-40) cc_final: 0.7241 (m110) REVERT: B 233 CYS cc_start: 0.7852 (t) cc_final: 0.7451 (t) REVERT: B 277 SER cc_start: 0.8187 (t) cc_final: 0.7620 (m) REVERT: B 304 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7521 (ttm170) REVERT: B 322 ASP cc_start: 0.6622 (t0) cc_final: 0.6325 (t0) REVERT: B 325 MET cc_start: 0.6820 (tpp) cc_final: 0.6589 (tpp) REVERT: D 121 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7065 (mtt) REVERT: D 137 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7513 (mt) REVERT: D 309 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7619 (mmmm) outliers start: 23 outliers final: 16 residues processed: 217 average time/residue: 0.2594 time to fit residues: 70.7939 Evaluate side-chains 219 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain P residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7344 Z= 0.221 Angle : 0.579 9.087 9962 Z= 0.295 Chirality : 0.043 0.167 1142 Planarity : 0.004 0.054 1261 Dihedral : 4.713 28.844 996 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.12 % Allowed : 19.90 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 905 helix: 1.83 (0.27), residues: 391 sheet: -0.92 (0.35), residues: 187 loop : 0.11 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS A 324 PHE 0.021 0.001 PHE D 198 TYR 0.010 0.001 TYR B 289 ARG 0.009 0.001 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7386 (mmtt) cc_final: 0.7135 (mmtt) REVERT: A 20 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6347 (mt-10) REVERT: A 26 ASP cc_start: 0.6736 (m-30) cc_final: 0.6307 (m-30) REVERT: A 186 GLU cc_start: 0.6685 (tt0) cc_final: 0.6446 (tt0) REVERT: A 329 HIS cc_start: 0.8098 (m170) cc_final: 0.7709 (m170) REVERT: A 359 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6204 (mt-10) REVERT: B 68 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7269 (ttt90) REVERT: B 83 ASP cc_start: 0.7604 (t0) cc_final: 0.7209 (t0) REVERT: B 101 MET cc_start: 0.7857 (mtp) cc_final: 0.7587 (mtp) REVERT: B 188 MET cc_start: 0.7201 (mmm) cc_final: 0.6831 (mmt) REVERT: B 196 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7680 (m) REVERT: B 214 ARG cc_start: 0.7489 (mpt90) cc_final: 0.6875 (mpt180) REVERT: B 219 ARG cc_start: 0.6884 (mmt180) cc_final: 0.6471 (mmt180) REVERT: B 230 ASN cc_start: 0.7629 (m-40) cc_final: 0.7352 (m110) REVERT: B 233 CYS cc_start: 0.7842 (t) cc_final: 0.7451 (t) REVERT: B 254 ASP cc_start: 0.6614 (t70) cc_final: 0.6231 (t0) REVERT: B 277 SER cc_start: 0.8197 (t) cc_final: 0.7641 (m) REVERT: B 304 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7533 (ttm170) REVERT: B 322 ASP cc_start: 0.6627 (t0) cc_final: 0.6364 (t0) REVERT: B 325 MET cc_start: 0.6867 (tpp) cc_final: 0.6584 (tpp) REVERT: D 115 LYS cc_start: 0.8013 (mttm) cc_final: 0.7780 (mttm) REVERT: D 121 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7060 (mtt) REVERT: D 137 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7552 (mt) REVERT: D 309 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7622 (mmmm) outliers start: 24 outliers final: 18 residues processed: 219 average time/residue: 0.2323 time to fit residues: 65.0334 Evaluate side-chains 231 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain P residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.0050 overall best weight: 0.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122067 restraints weight = 9559.485| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.14 r_work: 0.3372 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7344 Z= 0.185 Angle : 0.563 8.906 9962 Z= 0.288 Chirality : 0.043 0.160 1142 Planarity : 0.004 0.054 1261 Dihedral : 4.644 28.960 996 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.86 % Allowed : 20.42 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 905 helix: 1.93 (0.27), residues: 389 sheet: -0.86 (0.35), residues: 187 loop : 0.13 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS A 324 PHE 0.020 0.001 PHE D 198 TYR 0.009 0.001 TYR B 289 ARG 0.009 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.26 seconds wall clock time: 40 minutes 2.57 seconds (2402.57 seconds total)