Starting phenix.real_space_refine on Fri Oct 10 20:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uru_42501/10_2025/8uru_42501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uru_42501/10_2025/8uru_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uru_42501/10_2025/8uru_42501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uru_42501/10_2025/8uru_42501.map" model { file = "/net/cci-nas-00/data/ceres_data/8uru_42501/10_2025/8uru_42501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uru_42501/10_2025/8uru_42501.cif" } 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-2.0-5842/lib/python3.9/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: 2.31, per 1000 atoms: 0.26 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: 0.86 Conformation dependent library (CDL) restraints added in 316.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.04 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: 1.46 Time building geometry restraints manager: 1.06 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: 12257 2.68 - 5.37: 249 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: 1318 0.086 - 0.172: 98 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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= 0.271 Angle : 0.979 13.421 12553 Z= 0.565 Chirality : 0.050 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 aren 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 covalent geometry : bond 0.00464 ( 9159) covalent geometry : angle 0.97908 (12553) hydrogen bonds : bond 0.22871 ( 258) hydrogen bonds : angle 7.56729 ( 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 : 0.352 Fit side-chains revert: symmetry clash 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: 0.8111 (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: 0.8035 (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: 0.1104 time to fit residues: 24.7168 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 : 0.324 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN F 20 GLN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141464 restraints weight = 12542.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145152 restraints weight = 9809.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145673 restraints weight = 7188.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146178 restraints weight = 6205.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146585 restraints weight = 5874.745| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9159 Z= 0.145 Angle : 0.706 9.117 12553 Z= 0.366 Chirality : 0.044 0.252 1433 Planarity : 0.005 0.062 1426 Dihedral : 19.591 84.554 1569 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.59 % Favored : 89.78 % Rotamer: Outliers : 6.42 % Allowed : 27.24 % Favored : 66.33 % 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 aren not related in a simple way. whole: -2.46 (0.26), residues: 959 helix: 0.34 (0.33), residues: 244 sheet: -2.10 (0.36), residues: 176 loop : -2.51 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 155 TYR 0.012 0.001 TYR A 275 PHE 0.019 0.002 PHE B 11 TRP 0.011 0.001 TRP C 129 HIS 0.007 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9159) covalent geometry : angle 0.70617 (12553) hydrogen bonds : bond 0.03779 ( 258) hydrogen bonds : angle 5.55005 ( 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 200 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 142 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8251 (mt) cc_final: 0.7717 (mp) REVERT: B 47 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7564 (pp) REVERT: B 82 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6686 (pt0) REVERT: C 53 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7562 (p0) REVERT: C 173 LEU cc_start: 0.7764 (tp) cc_final: 0.7457 (tp) REVERT: F 25 GLU cc_start: 0.7881 (tp30) cc_final: 0.7608 (tp30) outliers start: 58 outliers final: 31 residues processed: 184 average time/residue: 0.0967 time to fit residues: 24.9317 Evaluate side-chains 158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 208 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 279 LEU 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 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 234 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 22 VAL 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 195 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 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 35 ASN 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: 0.2980 chunk 102 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN 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 = 0.181868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138829 restraints weight = 12671.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140396 restraints weight = 10351.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.141588 restraints weight = 9204.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142199 restraints weight = 7304.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142465 restraints weight = 6797.868| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1748 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= 0.148 Angle : 0.678 8.593 12553 Z= 0.350 Chirality : 0.043 0.261 1433 Planarity : 0.005 0.056 1426 Dihedral : 19.264 82.203 1542 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.80 % Favored : 89.78 % Rotamer: Outliers : 5.76 % Allowed : 29.46 % Favored : 64.78 % 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 aren not related in a simple way. whole: -2.30 (0.26), residues: 959 helix: 0.44 (0.34), residues: 248 sheet: -1.97 (0.35), residues: 187 loop : -2.43 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 13 TYR 0.012 0.001 TYR A 177 PHE 0.015 0.002 PHE B 77 TRP 0.023 0.001 TRP C 318 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9159) covalent geometry : angle 0.67813 (12553) hydrogen bonds : bond 0.03658 ( 258) hydrogen bonds : angle 5.25965 ( 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 189 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8303 (mt) cc_final: 0.8096 (mt) REVERT: A 387 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6377 (tmm) REVERT: B 82 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6850 (pt0) REVERT: C 52 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7054 (mmtm) REVERT: C 318 TRP cc_start: 0.7889 (m100) cc_final: 0.7628 (m100) REVERT: C 362 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7817 (m-10) outliers start: 52 outliers final: 26 residues processed: 176 average time/residue: 0.1083 time to fit residues: 25.9094 Evaluate side-chains 155 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 89 ARG 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 22 VAL 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 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 195 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.180264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137065 restraints weight = 12872.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137185 restraints weight = 10470.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138689 restraints weight = 9577.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139215 restraints weight = 7961.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139480 restraints weight = 7550.344| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9159 Z= 0.161 Angle : 0.691 9.391 12553 Z= 0.353 Chirality : 0.043 0.278 1433 Planarity : 0.005 0.069 1426 Dihedral : 19.127 81.668 1536 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.91 % Favored : 89.68 % Rotamer: Outliers : 5.54 % Allowed : 29.90 % Favored : 64.56 % 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 aren not related in a simple way. whole: -2.29 (0.26), residues: 959 helix: 0.49 (0.33), residues: 247 sheet: -1.94 (0.38), residues: 169 loop : -2.45 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.012 0.001 TYR A 177 PHE 0.020 0.002 PHE B 11 TRP 0.010 0.001 TRP C 153 HIS 0.005 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9159) covalent geometry : angle 0.69060 (12553) hydrogen bonds : bond 0.03614 ( 258) hydrogen bonds : angle 5.25080 ( 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 189 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8397 (pt) cc_final: 0.8029 (pt) REVERT: A 339 LEU cc_start: 0.8327 (mt) cc_final: 0.8095 (mt) REVERT: A 387 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6374 (tmm) REVERT: B 35 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7913 (mtp85) REVERT: B 47 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7543 (pp) REVERT: B 82 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6912 (pt0) REVERT: C 52 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7125 (mmtm) REVERT: C 318 TRP cc_start: 0.8020 (m100) cc_final: 0.7685 (m100) REVERT: C 332 HIS cc_start: 0.6474 (t-90) cc_final: 0.6269 (t-90) REVERT: C 362 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7883 (m-10) outliers start: 50 outliers final: 32 residues processed: 177 average time/residue: 0.0945 time to fit residues: 23.3758 Evaluate side-chains 168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 323 GLN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 387 MET 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 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 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 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 195 SER 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: 1.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 323 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN C 234 ASN F 15 GLN F 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137785 restraints weight = 12606.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138365 restraints weight = 9808.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139199 restraints weight = 10370.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140146 restraints weight = 7719.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140627 restraints weight = 6923.307| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9159 Z= 0.155 Angle : 0.685 8.052 12553 Z= 0.353 Chirality : 0.043 0.277 1433 Planarity : 0.005 0.058 1426 Dihedral : 19.010 79.074 1536 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.11 % Favored : 89.47 % Rotamer: Outliers : 6.64 % Allowed : 28.57 % Favored : 64.78 % 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 aren not related in a simple way. whole: -2.39 (0.26), residues: 959 helix: 0.46 (0.33), residues: 252 sheet: -2.35 (0.36), residues: 179 loop : -2.41 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.013 0.001 TYR A 177 PHE 0.012 0.001 PHE B 77 TRP 0.010 0.001 TRP C 129 HIS 0.005 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9159) covalent geometry : angle 0.68482 (12553) hydrogen bonds : bond 0.03485 ( 258) hydrogen bonds : angle 5.18175 ( 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 198 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 339 LEU cc_start: 0.8299 (mt) cc_final: 0.8059 (mt) REVERT: A 387 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6390 (tmm) REVERT: B 47 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7552 (pp) REVERT: B 82 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6887 (pt0) REVERT: C 52 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7152 (mmtm) REVERT: C 318 TRP cc_start: 0.8043 (m100) cc_final: 0.7740 (m100) REVERT: F 16 ASP cc_start: 0.7445 (t0) cc_final: 0.7114 (t0) outliers start: 60 outliers final: 31 residues processed: 183 average time/residue: 0.0922 time to fit residues: 23.7805 Evaluate side-chains 168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR 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 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 68 VAL 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 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN 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 = 0.4186 r_free = 0.4186 target = 0.174513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133313 restraints weight = 13179.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133133 restraints weight = 10876.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134238 restraints weight = 9847.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137684 restraints weight = 8818.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137719 restraints weight = 7206.553| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9159 Z= 0.233 Angle : 0.747 9.097 12553 Z= 0.387 Chirality : 0.046 0.318 1433 Planarity : 0.005 0.057 1426 Dihedral : 19.038 80.918 1536 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.89 % Favored : 87.70 % Rotamer: Outliers : 6.20 % Allowed : 29.57 % Favored : 64.23 % 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 aren not related in a simple way. whole: -2.42 (0.26), residues: 959 helix: 0.35 (0.33), residues: 242 sheet: -2.39 (0.35), residues: 189 loop : -2.31 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 199 TYR 0.016 0.002 TYR A 177 PHE 0.023 0.002 PHE B 11 TRP 0.009 0.001 TRP C 153 HIS 0.007 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9159) covalent geometry : angle 0.74718 (12553) hydrogen bonds : bond 0.04172 ( 258) hydrogen bonds : angle 5.36087 ( 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 191 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7710 (ttp80) REVERT: A 220 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6550 (tttm) REVERT: A 339 LEU cc_start: 0.8265 (mt) cc_final: 0.7983 (mt) REVERT: A 387 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6420 (tmm) REVERT: B 47 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 82 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6863 (pt0) REVERT: C 52 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7156 (mmtm) REVERT: F 16 ASP cc_start: 0.7417 (t0) cc_final: 0.7105 (t0) outliers start: 56 outliers final: 37 residues processed: 178 average time/residue: 0.0946 time to fit residues: 23.4949 Evaluate side-chains 167 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR 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 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 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 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 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 Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** 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 = 0.4231 r_free = 0.4231 target = 0.180861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138470 restraints weight = 12768.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138729 restraints weight = 10003.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140326 restraints weight = 9578.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140875 restraints weight = 7589.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141245 restraints weight = 7073.407| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9159 Z= 0.133 Angle : 0.679 8.223 12553 Z= 0.350 Chirality : 0.043 0.264 1433 Planarity : 0.005 0.078 1426 Dihedral : 18.821 74.365 1536 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.76 % Favored : 90.72 % Rotamer: Outliers : 4.98 % Allowed : 30.68 % Favored : 64.34 % 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 aren not related in a simple way. whole: -2.20 (0.26), residues: 959 helix: 0.78 (0.34), residues: 240 sheet: -2.41 (0.34), residues: 176 loop : -2.25 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.016 0.001 TYR A 177 PHE 0.013 0.001 PHE A 156 TRP 0.033 0.002 TRP C 318 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9159) covalent geometry : angle 0.67884 (12553) hydrogen bonds : bond 0.03364 ( 258) hydrogen bonds : angle 5.21702 ( 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 182 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7974 (mt) REVERT: B 47 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7655 (pp) REVERT: B 82 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6824 (pt0) REVERT: F 16 ASP cc_start: 0.7448 (t0) cc_final: 0.7161 (t0) REVERT: F 25 GLU cc_start: 0.8136 (tp30) cc_final: 0.7854 (tp30) outliers start: 45 outliers final: 33 residues processed: 168 average time/residue: 0.0965 time to fit residues: 22.8306 Evaluate side-chains 165 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 253 MET 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 B residue 47 LEU Chi-restraints excluded: chain B residue 77 PHE 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 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 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 315 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.0020 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN F 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.180506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137912 restraints weight = 12472.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138007 restraints weight = 10004.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139435 restraints weight = 9364.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140072 restraints weight = 7724.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140343 restraints weight = 7276.892| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9159 Z= 0.143 Angle : 0.700 12.003 12553 Z= 0.355 Chirality : 0.043 0.278 1433 Planarity : 0.005 0.071 1426 Dihedral : 18.767 72.785 1536 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.18 % Favored : 90.30 % Rotamer: Outliers : 5.43 % Allowed : 31.45 % 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 aren not related in a simple way. whole: -2.11 (0.27), residues: 959 helix: 0.87 (0.35), residues: 241 sheet: -2.27 (0.34), residues: 189 loop : -2.22 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 13 TYR 0.015 0.001 TYR A 177 PHE 0.023 0.001 PHE B 11 TRP 0.029 0.001 TRP C 318 HIS 0.005 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9159) covalent geometry : angle 0.69965 (12553) hydrogen bonds : bond 0.03350 ( 258) hydrogen bonds : angle 5.08638 ( 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 193 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7290 (ttp80) REVERT: A 61 GLU cc_start: 0.7183 (pp20) cc_final: 0.6774 (tm-30) REVERT: A 220 LYS cc_start: 0.7233 (mmtt) cc_final: 0.6452 (tttm) REVERT: A 339 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 47 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 61 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7446 (pp) REVERT: B 82 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6823 (pt0) REVERT: C 106 LYS cc_start: 0.4950 (OUTLIER) cc_final: 0.4694 (pttm) REVERT: C 119 MET cc_start: 0.7220 (tpp) cc_final: 0.7018 (tpp) REVERT: F 16 ASP cc_start: 0.7432 (t0) cc_final: 0.7181 (t0) REVERT: F 25 GLU cc_start: 0.8247 (tp30) cc_final: 0.7958 (tp30) outliers start: 49 outliers final: 37 residues processed: 179 average time/residue: 0.0975 time to fit residues: 24.3992 Evaluate side-chains 178 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 287 THR 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 B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR 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 106 LYS 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 195 SER Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS 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 24 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 62 optimal weight: 0.0060 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.182816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140524 restraints weight = 12490.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140416 restraints weight = 9687.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142000 restraints weight = 9355.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142678 restraints weight = 7639.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142967 restraints weight = 7108.932| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9159 Z= 0.126 Angle : 0.674 9.451 12553 Z= 0.345 Chirality : 0.042 0.276 1433 Planarity : 0.005 0.085 1426 Dihedral : 18.672 71.378 1536 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.34 % Favored : 91.14 % Rotamer: Outliers : 5.20 % Allowed : 31.01 % Favored : 63.79 % 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 aren not related in a simple way. whole: -2.01 (0.27), residues: 959 helix: 0.98 (0.35), residues: 241 sheet: -2.19 (0.33), residues: 199 loop : -2.17 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.016 0.001 TYR A 177 PHE 0.012 0.001 PHE B 77 TRP 0.027 0.001 TRP C 318 HIS 0.009 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9159) covalent geometry : angle 0.67384 (12553) hydrogen bonds : bond 0.03159 ( 258) hydrogen bonds : angle 5.00507 ( 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 190 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7175 (pp20) cc_final: 0.6808 (tm-30) REVERT: A 219 ILE cc_start: 0.8195 (pt) cc_final: 0.7812 (pt) REVERT: A 220 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6529 (tttm) REVERT: A 339 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (mt) REVERT: B 47 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7645 (pp) REVERT: B 61 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7429 (pp) REVERT: B 82 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6849 (pt0) REVERT: F 16 ASP cc_start: 0.7456 (t0) cc_final: 0.7216 (t0) outliers start: 47 outliers final: 33 residues processed: 178 average time/residue: 0.1030 time to fit residues: 25.1275 Evaluate side-chains 168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 339 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 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 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 315 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 377 GLU 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 22 PHE 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: 3.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.179291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136668 restraints weight = 12677.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136844 restraints weight = 10025.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137932 restraints weight = 10610.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138796 restraints weight = 7913.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139295 restraints weight = 7162.377| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9159 Z= 0.164 Angle : 0.731 11.668 12553 Z= 0.369 Chirality : 0.044 0.280 1433 Planarity : 0.005 0.081 1426 Dihedral : 18.708 72.439 1534 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.22 % Favored : 89.16 % Rotamer: Outliers : 5.32 % Allowed : 31.56 % 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 aren not related in a simple way. whole: -2.04 (0.26), residues: 959 helix: 1.02 (0.35), residues: 235 sheet: -2.23 (0.33), residues: 196 loop : -2.18 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 13 TYR 0.016 0.002 TYR A 177 PHE 0.022 0.002 PHE B 11 TRP 0.026 0.001 TRP C 318 HIS 0.009 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9159) covalent geometry : angle 0.73115 (12553) hydrogen bonds : bond 0.03508 ( 258) hydrogen bonds : angle 5.04060 ( 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 184 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7837 (ttp80) REVERT: A 61 GLU cc_start: 0.7234 (pp20) cc_final: 0.6869 (tm-30) REVERT: A 219 ILE cc_start: 0.8296 (pt) cc_final: 0.7903 (pt) REVERT: A 220 LYS cc_start: 0.7337 (mmtt) cc_final: 0.6586 (tttm) REVERT: A 339 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7953 (mt) REVERT: B 47 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7651 (pp) REVERT: B 61 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7568 (pp) REVERT: B 82 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6892 (pt0) REVERT: F 16 ASP cc_start: 0.7442 (t0) cc_final: 0.7200 (t0) outliers start: 48 outliers final: 39 residues processed: 172 average time/residue: 0.0959 time to fit residues: 23.1321 Evaluate side-chains 176 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 172 GLN 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 339 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU 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 116 THR 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 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 315 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 34 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.0010 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 0.0040 chunk 92 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136725 restraints weight = 12542.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136668 restraints weight = 9998.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138009 restraints weight = 10198.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138756 restraints weight = 7932.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139094 restraints weight = 7316.597| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 9159 Z= 0.330 Angle : 1.139 59.183 12553 Z= 0.684 Chirality : 0.048 0.789 1433 Planarity : 0.007 0.145 1426 Dihedral : 18.723 72.408 1534 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.32 % Favored : 89.16 % Rotamer: Outliers : 4.87 % Allowed : 31.45 % Favored : 63.68 % Cbeta Deviations : 0.21 % 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 aren not related in a simple way. whole: -2.03 (0.27), residues: 959 helix: 1.03 (0.35), residues: 235 sheet: -2.23 (0.33), residues: 196 loop : -2.18 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.013 0.001 TYR A 177 PHE 0.014 0.002 PHE B 11 TRP 0.023 0.001 TRP C 318 HIS 0.008 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 9159) covalent geometry : angle 1.13881 (12553) hydrogen bonds : bond 0.03473 ( 258) hydrogen bonds : angle 5.04151 ( 673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.58 seconds wall clock time: 28 minutes 15.36 seconds (1695.36 seconds total)