Starting phenix.real_space_refine on Wed Aug 5 06:19:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uru_42501/08_2026/8uru_42501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uru_42501/08_2026/8uru_42501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uru_42501/08_2026/8uru_42501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uru_42501/08_2026/8uru_42501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uru_42501/08_2026/8uru_42501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uru_42501/08_2026/8uru_42501.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 5555 2.51 5 N 1517 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2913 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 347} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1860 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain breaks: 4 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.18 Number of scatterers: 8895 At special positions: 0 Unit cell: (110.656, 111.72, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 43 15.00 Mg 1 11.99 O 1742 8.00 N 1517 7.00 C 5555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 272.1 milliseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 28.5% alpha, 12.8% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.651A pdb=" N SER A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.623A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.691A pdb=" N PHE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.044A pdb=" N VAL A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 5.288A pdb=" N ASN A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 320 through 328 removed outlier: 6.174A pdb=" N LEU A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.607A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 134 removed outlier: 4.393A pdb=" N LEU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 134' Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.968A pdb=" N TYR B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.930A pdb=" N ILE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.848A pdb=" N ALA B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.588A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.576A pdb=" N ASP C 335 " --> pdb=" O HIS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.662A pdb=" N LEU F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 20 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 32 removed outlier: 4.145A pdb=" N GLN F 30 " --> pdb=" O ARG F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.545A pdb=" N THR F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN F 58 " --> pdb=" O MET F 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.953A pdb=" N ARG A 25 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 70 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 27 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLN A 72 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.409A pdb=" N THR A 128 " --> pdb=" O ILE A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5 removed outlier: 4.337A pdb=" N ARG B 35 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 49 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 148 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.037A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.512A pdb=" N LEU C 38 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 40 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 56 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.557A pdb=" N LEU C 83 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N CYS C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 130 removed outlier: 3.742A pdb=" N ALA C 126 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 141 " --> pdb=" O TRP C 153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 151 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.510A pdb=" N ILE C 200 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 210 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 250 through 254 removed outlier: 3.507A pdb=" N CYS C 259 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 260 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 296 removed outlier: 6.682A pdb=" N ALA C 309 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 316 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY C 310 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 315 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 328 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE C 317 " --> pdb=" O ILE C 326 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1379 1.32 - 1.44: 2675 1.44 - 1.57: 4967 1.57 - 1.70: 84 1.70 - 1.83: 54 Bond restraints: 9159 Sorted by residual: bond pdb=" CA PHE A 91 " pdb=" C PHE A 91 " ideal model delta sigma weight residual 1.525 1.483 0.042 1.07e-02 8.73e+03 1.51e+01 bond pdb=" C LEU A 175 " pdb=" O LEU A 175 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.28e-02 6.10e+03 1.14e+01 bond pdb=" C PHE A 91 " pdb=" O PHE A 91 " ideal model delta sigma weight residual 1.245 1.198 0.047 1.53e-02 4.27e+03 9.58e+00 bond pdb=" CA ASP A 90 " pdb=" C ASP A 90 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.37e-02 5.33e+03 8.95e+00 bond pdb=" CA LEU B 221 " pdb=" C LEU B 221 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.26e-02 6.30e+03 7.94e+00 ... (remaining 9154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12255 2.68 - 5.37: 251 5.37 - 8.05: 27 8.05 - 10.74: 17 10.74 - 13.42: 3 Bond angle restraints: 12553 Sorted by residual: angle pdb=" C TYR B 188 " pdb=" N PRO B 189 " pdb=" CA PRO B 189 " ideal model delta sigma weight residual 119.84 131.45 -11.61 1.25e+00 6.40e-01 8.62e+01 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 110.97 123.31 -12.34 1.56e+00 4.11e-01 6.26e+01 angle pdb=" N ALA A 171 " pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 113.19 121.97 -8.78 1.19e+00 7.06e-01 5.44e+01 angle pdb=" N SER B 196 " pdb=" CA SER B 196 " pdb=" C SER B 196 " ideal model delta sigma weight residual 112.93 104.56 8.37 1.33e+00 5.65e-01 3.96e+01 angle pdb=" C ILE A 353 " pdb=" CA ILE A 353 " pdb=" CB ILE A 353 " ideal model delta sigma weight residual 111.06 105.69 5.37 8.80e-01 1.29e+00 3.72e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4200 17.88 - 35.76: 790 35.76 - 53.64: 312 53.64 - 71.51: 68 71.51 - 89.39: 10 Dihedral angle restraints: 5380 sinusoidal: 2451 harmonic: 2929 Sorted by residual: dihedral pdb=" CA SER B 218 " pdb=" C SER B 218 " pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual 180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CA GLN A 172 " pdb=" CB GLN A 172 " ideal model delta harmonic sigma weight residual 122.80 133.33 -10.53 0 2.50e+00 1.60e-01 1.77e+01 ... (remaining 5377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1316 0.086 - 0.172: 100 0.172 - 0.258: 13 0.258 - 0.344: 2 0.344 - 0.431: 2 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA GLN A 172 " pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CB GLN A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU B 221 " pdb=" N LEU B 221 " pdb=" C LEU B 221 " pdb=" CB LEU B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1430 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 91 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C GLY C 91 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY C 91 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP C 92 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 242 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO C 243 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 77 " 0.025 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE B 77 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 77 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 77 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 77 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 77 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 142 2.63 - 3.19: 7855 3.19 - 3.76: 13789 3.76 - 4.33: 18078 4.33 - 4.90: 28991 Nonbonded interactions: 68855 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb="MG MG A 501 " model vdw 2.058 2.170 nonbonded pdb=" OD2 ASP A 290 " pdb="MG MG A 501 " model vdw 2.122 2.170 nonbonded pdb=" O ILE B 165 " pdb=" OG SER B 166 " model vdw 2.183 3.040 nonbonded pdb=" N GLN F 30 " pdb=" OE1 GLN F 30 " model vdw 2.217 3.120 nonbonded pdb=" O LYS A 173 " pdb=" NZ LYS A 173 " model vdw 2.221 3.120 ... (remaining 68850 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.005 0.064 9159 Z= 0.340 Angle : 0.999 13.421 12553 Z= 0.616 Chirality : 0.052 0.431 1433 Planarity : 0.006 0.068 1426 Dihedral : 21.437 89.392 3460 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.95 % Favored : 88.11 % Rotamer: Outliers : 3.21 % Allowed : 33.22 % Favored : 63.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.25), residues: 959 helix: -0.16 (0.34), residues: 244 sheet: -2.19 (0.37), residues: 176 loop : -2.88 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.014 0.001 TYR A 275 PHE 0.041 0.002 PHE B 77 TRP 0.025 0.002 TRP C 41 HIS 0.011 0.001 HIS C 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.34 ( 9159) covalent geometry : angle 0.99907 / 0.62 (12553) hydrogen bonds : bond 0.22871 / 15.28 ( 258) hydrogen bonds : angle 7.56729 / 5.64 ( 673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7707 (mtpt) REVERT: A 378 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 47 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7633 (pp) REVERT: B 82 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6861 (pt0) REVERT: B 184 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 192 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: B 221 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7131 (tt) REVERT: C 53 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7110 (p0) outliers start: 29 outliers final: 16 residues processed: 165 average time/residue: 0.0873 time to fit residues: 19.7064 Evaluate side-chains 143 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 122 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0770 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN F 15 GLN F 20 GLN ** F 35 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 = 0.4262 r_free = 0.4262 target = 0.183590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141621 restraints weight = 12515.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145537 restraints weight = 9761.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146113 restraints weight = 6914.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146407 restraints weight = 6014.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146810 restraints weight = 5776.182| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9159 Z= 0.158 Angle : 0.760 9.702 12553 Z= 0.392 Chirality : 0.046 0.218 1433 Planarity : 0.005 0.063 1426 Dihedral : 20.015 86.734 1569 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.91 % Favored : 89.47 % Rotamer: Outliers : 4.87 % Allowed : 29.24 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.26), residues: 959 helix: 0.27 (0.33), residues: 246 sheet: -2.12 (0.36), residues: 176 loop : -2.67 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 155 TYR 0.009 0.001 TYR A 177 PHE 0.020 0.002 PHE B 11 TRP 0.010 0.001 TRP C 129 HIS 0.010 0.001 HIS C 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 9159) covalent geometry : angle 0.76004 / 0.39 (12553) hydrogen bonds : bond 0.05102 / 3.44 ( 258) hydrogen bonds : angle 5.84924 / 4.27 ( 673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7863 (p0) cc_final: 0.7627 (p0) REVERT: B 47 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7558 (pp) REVERT: B 82 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6683 (pt0) REVERT: B 128 SER cc_start: 0.7702 (OUTLIER) cc_final: 0.7483 (p) REVERT: C 53 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7492 (p0) REVERT: C 173 LEU cc_start: 0.7709 (tp) cc_final: 0.7397 (tp) REVERT: C 229 MET cc_start: 0.4922 (ppp) cc_final: 0.4700 (ppp) REVERT: F 25 GLU cc_start: 0.7740 (tp30) cc_final: 0.7519 (tp30) outliers start: 44 outliers final: 26 residues processed: 174 average time/residue: 0.0752 time to fit residues: 18.2725 Evaluate side-chains 158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.0020 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139113 restraints weight = 12657.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142226 restraints weight = 10424.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143012 restraints weight = 7659.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143361 restraints weight = 6682.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144000 restraints weight = 6355.535| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9159 Z= 0.144 Angle : 0.707 11.013 12553 Z= 0.363 Chirality : 0.045 0.239 1433 Planarity : 0.005 0.059 1426 Dihedral : 19.754 85.726 1549 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.01 % Favored : 89.47 % Rotamer: Outliers : 5.98 % Allowed : 28.90 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.26), residues: 959 helix: 0.40 (0.33), residues: 245 sheet: -1.92 (0.35), residues: 187 loop : -2.52 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 325 TYR 0.011 0.001 TYR A 275 PHE 0.016 0.002 PHE B 77 TRP 0.035 0.002 TRP C 318 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9159) covalent geometry : angle 0.70705 / 0.36 (12553) hydrogen bonds : bond 0.04135 / 2.79 ( 258) hydrogen bonds : angle 5.47769 / 4.01 ( 673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8310 (mt) cc_final: 0.8105 (mt) REVERT: A 353 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8718 (tt) REVERT: B 47 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 82 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6696 (pt0) REVERT: C 53 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7536 (p0) REVERT: C 173 LEU cc_start: 0.7784 (tp) cc_final: 0.7445 (tp) REVERT: C 362 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7748 (m-10) REVERT: C 377 GLU cc_start: 0.5869 (tt0) cc_final: 0.5561 (tt0) REVERT: F 25 GLU cc_start: 0.7881 (tp30) cc_final: 0.7621 (tp30) outliers start: 54 outliers final: 27 residues processed: 169 average time/residue: 0.0762 time to fit residues: 18.0567 Evaluate side-chains 153 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 362 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.181294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138715 restraints weight = 12860.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140376 restraints weight = 10392.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141435 restraints weight = 9210.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142084 restraints weight = 7223.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142525 restraints weight = 6745.763| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9159 Z= 0.154 Angle : 0.706 9.398 12553 Z= 0.361 Chirality : 0.044 0.258 1433 Planarity : 0.005 0.055 1426 Dihedral : 19.694 86.153 1542 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.11 % Favored : 89.47 % Rotamer: Outliers : 5.76 % Allowed : 30.34 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.26), residues: 959 helix: 0.50 (0.33), residues: 245 sheet: -1.94 (0.35), residues: 192 loop : -2.53 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 325 TYR 0.012 0.001 TYR A 275 PHE 0.017 0.002 PHE A 238 TRP 0.039 0.002 TRP C 318 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9159) covalent geometry : angle 0.70619 / 0.36 (12553) hydrogen bonds : bond 0.03812 / 2.56 ( 258) hydrogen bonds : angle 5.36810 / 3.93 ( 673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8361 (mt) cc_final: 0.8136 (mt) REVERT: B 47 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7490 (pp) REVERT: B 82 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6738 (pt0) REVERT: C 53 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7750 (p0) REVERT: C 362 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7841 (m-10) REVERT: F 25 GLU cc_start: 0.7964 (tp30) cc_final: 0.7617 (tp30) outliers start: 52 outliers final: 33 residues processed: 164 average time/residue: 0.0718 time to fit residues: 16.7299 Evaluate side-chains 161 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 362 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 250 GLN ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.179195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136558 restraints weight = 12663.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137200 restraints weight = 10398.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139217 restraints weight = 9149.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139585 restraints weight = 7221.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139873 restraints weight = 6900.246| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9159 Z= 0.186 Angle : 0.723 9.860 12553 Z= 0.370 Chirality : 0.045 0.280 1433 Planarity : 0.005 0.056 1426 Dihedral : 19.676 86.532 1542 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.74 % Favored : 88.84 % Rotamer: Outliers : 6.98 % Allowed : 29.90 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.26), residues: 959 helix: 0.50 (0.33), residues: 245 sheet: -1.95 (0.38), residues: 169 loop : -2.53 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 325 TYR 0.012 0.001 TYR A 275 PHE 0.016 0.002 PHE C 59 TRP 0.018 0.001 TRP C 318 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 9159) covalent geometry : angle 0.72287 / 0.37 (12553) hydrogen bonds : bond 0.03960 / 2.66 ( 258) hydrogen bonds : angle 5.38771 / 3.94 ( 673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 129 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8382 (mt) cc_final: 0.8160 (mt) REVERT: B 47 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7489 (pp) REVERT: B 82 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6766 (pt0) REVERT: C 52 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.7003 (mmtm) REVERT: C 53 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7733 (p0) REVERT: C 56 TYR cc_start: 0.8314 (m-10) cc_final: 0.7801 (m-10) REVERT: F 25 GLU cc_start: 0.8106 (tp30) cc_final: 0.7765 (tp30) outliers start: 63 outliers final: 43 residues processed: 176 average time/residue: 0.0758 time to fit residues: 18.8154 Evaluate side-chains 166 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 40.0000 chunk 57 optimal weight: 4.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 35 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 = 0.4179 r_free = 0.4179 target = 0.175629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132716 restraints weight = 12722.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133021 restraints weight = 10505.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134356 restraints weight = 10243.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135000 restraints weight = 7846.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135455 restraints weight = 7188.078| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9159 Z= 0.240 Angle : 0.763 11.013 12553 Z= 0.394 Chirality : 0.047 0.295 1433 Planarity : 0.005 0.074 1426 Dihedral : 19.675 87.640 1540 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.99 % Favored : 87.49 % Rotamer: Outliers : 7.97 % Allowed : 29.46 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.25), residues: 959 helix: 0.30 (0.32), residues: 249 sheet: -2.05 (0.37), residues: 173 loop : -2.58 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 244 TYR 0.015 0.002 TYR A 177 PHE 0.021 0.002 PHE B 11 TRP 0.019 0.002 TRP C 318 HIS 0.006 0.001 HIS C 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 ( 9159) covalent geometry : angle 0.76316 / 0.39 (12553) hydrogen bonds : bond 0.04375 / 2.95 ( 258) hydrogen bonds : angle 5.47095 / 4.01 ( 673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 129 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8342 (mt) cc_final: 0.8074 (mt) REVERT: B 47 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7558 (pp) REVERT: B 82 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6791 (pt0) REVERT: B 245 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6484 (mtt90) REVERT: C 52 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7058 (mmtm) REVERT: C 53 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7812 (p0) REVERT: F 25 GLU cc_start: 0.8192 (tp30) cc_final: 0.7823 (tp30) outliers start: 72 outliers final: 47 residues processed: 187 average time/residue: 0.0726 time to fit residues: 19.2440 Evaluate side-chains 172 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS F 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.179923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137547 restraints weight = 12727.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138019 restraints weight = 10087.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139517 restraints weight = 9799.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140105 restraints weight = 7481.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140493 restraints weight = 6991.418| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9159 Z= 0.140 Angle : 0.718 10.087 12553 Z= 0.367 Chirality : 0.044 0.237 1433 Planarity : 0.005 0.079 1426 Dihedral : 19.517 82.797 1540 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.70 % Favored : 89.78 % Rotamer: Outliers : 6.53 % Allowed : 30.90 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.26), residues: 959 helix: 0.67 (0.34), residues: 245 sheet: -1.99 (0.37), residues: 174 loop : -2.49 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 244 TYR 0.022 0.001 TYR A 275 PHE 0.012 0.001 PHE B 77 TRP 0.020 0.001 TRP C 318 HIS 0.006 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9159) covalent geometry : angle 0.71800 / 0.37 (12553) hydrogen bonds : bond 0.03692 / 2.46 ( 258) hydrogen bonds : angle 5.30130 / 3.88 ( 673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8283 (mt) cc_final: 0.8019 (mt) REVERT: B 47 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7528 (pp) REVERT: B 82 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6810 (pt0) REVERT: B 245 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6382 (mtt90) REVERT: F 25 GLU cc_start: 0.8098 (tp30) cc_final: 0.7752 (tp30) outliers start: 59 outliers final: 37 residues processed: 175 average time/residue: 0.0759 time to fit residues: 19.1418 Evaluate side-chains 159 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138389 restraints weight = 12639.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138530 restraints weight = 10192.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140101 restraints weight = 9599.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140705 restraints weight = 7823.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141050 restraints weight = 7289.938| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9159 Z= 0.133 Angle : 0.706 9.629 12553 Z= 0.362 Chirality : 0.045 0.259 1433 Planarity : 0.005 0.073 1426 Dihedral : 19.457 81.398 1538 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.59 % Favored : 89.78 % Rotamer: Outliers : 5.32 % Allowed : 32.23 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.26), residues: 959 helix: 0.73 (0.34), residues: 246 sheet: -1.97 (0.36), residues: 174 loop : -2.47 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.018 0.001 TYR A 275 PHE 0.022 0.002 PHE B 11 TRP 0.019 0.001 TRP C 318 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9159) covalent geometry : angle 0.70602 / 0.36 (12553) hydrogen bonds : bond 0.03505 / 2.34 ( 258) hydrogen bonds : angle 5.27086 / 3.86 ( 673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.7631 (mt) cc_final: 0.7306 (mt) REVERT: A 220 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7479 (mmtt) REVERT: B 82 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6852 (pt0) REVERT: C 52 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7033 (mmtm) REVERT: F 16 ASP cc_start: 0.7636 (t0) cc_final: 0.7277 (t0) outliers start: 48 outliers final: 31 residues processed: 168 average time/residue: 0.0778 time to fit residues: 18.0619 Evaluate side-chains 156 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 388 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.180405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137713 restraints weight = 12618.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137990 restraints weight = 10083.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139467 restraints weight = 9377.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140052 restraints weight = 7725.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140312 restraints weight = 7308.631| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9159 Z= 0.145 Angle : 0.722 11.498 12553 Z= 0.368 Chirality : 0.044 0.282 1433 Planarity : 0.005 0.070 1426 Dihedral : 19.397 80.991 1536 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.49 % Favored : 89.89 % Rotamer: Outliers : 5.20 % Allowed : 32.00 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.26), residues: 959 helix: 0.66 (0.34), residues: 247 sheet: -2.33 (0.34), residues: 190 loop : -2.40 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 244 TYR 0.018 0.001 TYR A 275 PHE 0.014 0.001 PHE B 77 TRP 0.021 0.001 TRP C 318 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9159) covalent geometry : angle 0.72208 / 0.37 (12553) hydrogen bonds : bond 0.03591 / 2.41 ( 258) hydrogen bonds : angle 5.24287 / 3.83 ( 673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7769 (ttp80) REVERT: A 339 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8026 (mt) REVERT: B 82 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6858 (pt0) REVERT: C 119 MET cc_start: 0.7220 (tpp) cc_final: 0.7016 (tpp) REVERT: F 16 ASP cc_start: 0.7561 (t0) cc_final: 0.7238 (t0) outliers start: 47 outliers final: 36 residues processed: 165 average time/residue: 0.0671 time to fit residues: 15.9116 Evaluate side-chains 164 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 382 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.181869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138879 restraints weight = 12947.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139065 restraints weight = 10677.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140766 restraints weight = 9717.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141278 restraints weight = 7903.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141526 restraints weight = 7546.365| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9159 Z= 0.131 Angle : 0.701 9.492 12553 Z= 0.358 Chirality : 0.043 0.264 1433 Planarity : 0.005 0.089 1426 Dihedral : 19.327 78.526 1536 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.97 % Favored : 90.41 % Rotamer: Outliers : 4.65 % Allowed : 33.00 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.26), residues: 959 helix: 0.88 (0.35), residues: 241 sheet: -2.44 (0.33), residues: 178 loop : -2.27 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 244 TYR 0.015 0.001 TYR A 275 PHE 0.023 0.001 PHE B 77 TRP 0.020 0.001 TRP C 318 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9159) covalent geometry : angle 0.70096 / 0.36 (12553) hydrogen bonds : bond 0.03466 / 2.32 ( 258) hydrogen bonds : angle 5.21097 / 3.82 ( 673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.7618 (mt) cc_final: 0.7291 (mt) REVERT: A 220 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6310 (tttm) REVERT: A 339 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7996 (mt) REVERT: B 47 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7516 (pp) REVERT: B 82 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6763 (pt0) REVERT: F 16 ASP cc_start: 0.7662 (t0) cc_final: 0.7306 (t0) outliers start: 42 outliers final: 36 residues processed: 160 average time/residue: 0.0725 time to fit residues: 16.7367 Evaluate side-chains 164 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.181460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139728 restraints weight = 12681.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139929 restraints weight = 10047.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141414 restraints weight = 10148.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141999 restraints weight = 7571.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142499 restraints weight = 7092.595| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.235 9159 Z= 0.334 Angle : 1.218 59.200 12553 Z= 0.742 Chirality : 0.047 0.578 1433 Planarity : 0.005 0.087 1426 Dihedral : 19.341 78.521 1536 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.97 % Favored : 90.41 % Rotamer: Outliers : 4.76 % Allowed : 33.00 % Favored : 62.24 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.26), residues: 959 helix: 0.88 (0.35), residues: 241 sheet: -2.44 (0.33), residues: 178 loop : -2.27 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.013 0.001 TYR A 275 PHE 0.022 0.001 PHE B 77 TRP 0.018 0.001 TRP C 318 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.33 ( 9159) covalent geometry : angle 1.21830 / 0.74 (12553) hydrogen bonds : bond 0.03456 / 2.31 ( 258) hydrogen bonds : angle 5.21013 / 3.82 ( 673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1262.05 seconds wall clock time: 22 minutes 30.09 seconds (1350.09 seconds total)