Starting phenix.real_space_refine on Tue Mar 3 14:48:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eg0_28108/03_2026/8eg0_28108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eg0_28108/03_2026/8eg0_28108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eg0_28108/03_2026/8eg0_28108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eg0_28108/03_2026/8eg0_28108.map" model { file = "/net/cci-nas-00/data/ceres_data/8eg0_28108/03_2026/8eg0_28108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eg0_28108/03_2026/8eg0_28108.cif" } resolution = 3.53 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= 0.005 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 23 5.16 5 C 3592 2.51 5 N 1056 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6031 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2733 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 1882 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1865 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 230, 1865 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 1900 Chain: "C" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1390 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 26, 'rna3p_pyr': 26} Link IDs: {'rna2p': 13, 'rna3p': 51} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.25 Number of scatterers: 6031 At special positions: 0 Unit cell: (69.72, 95.865, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 65 15.00 O 1295 8.00 N 1056 7.00 C 3592 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: 0.63 Conformation dependent library (CDL) restraints added in 242.8 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1098 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 8 sheets defined 25.2% alpha, 30.5% beta 25 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.856A pdb=" N GLN B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 352 through 361 removed outlier: 4.262A pdb=" N SER B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.569A pdb=" N SER B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.604A pdb=" N PHE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.503A pdb=" N LYS A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 4.107A pdb=" N ALA A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.754A pdb=" N SER A 226 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 4.253A pdb=" N GLY A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 69 removed outlier: 6.966A pdb=" N THR B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER B 67 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 77 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 69 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B 75 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 85 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 98 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 87 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.521A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 142 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER B 128 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 140 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 153 removed outlier: 3.708A pdb=" N ASP B 150 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 169 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TRP B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE B 180 " --> pdb=" O TRP B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.711A pdb=" N ARG B 193 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 208 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU B 217 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN B 223 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 252 removed outlier: 3.530A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS B 262 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 267 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN B 272 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 282 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP B 274 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU B 280 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 292 through 298 removed outlier: 3.855A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 138 removed outlier: 5.042A pdb=" N VAL A 78 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 104 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 80 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU A 106 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP A 82 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLU A 79 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N MET A 157 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 81 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE A 159 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 83 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 154 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY A 191 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS A 156 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 193 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE A 158 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR A 195 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU A 160 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 197 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG A 258 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 193 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 256 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 195 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 254 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 197 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 252 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1621 1.34 - 1.45: 1492 1.45 - 1.57: 3036 1.57 - 1.69: 128 1.69 - 1.81: 31 Bond restraints: 6308 Sorted by residual: bond pdb=" C2 SAH A 301 " pdb=" N3 SAH A 301 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C8 SAH A 301 " pdb=" N7 SAH A 301 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C2 SAH A 301 " pdb=" N1 SAH A 301 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C6 SAH A 301 " pdb=" N1 SAH A 301 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1' SAH A 301 " pdb=" N9 SAH A 301 " ideal model delta sigma weight residual 1.440 1.474 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 6303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 8813 2.40 - 4.79: 47 4.79 - 7.19: 3 7.19 - 9.59: 3 9.59 - 11.98: 1 Bond angle restraints: 8867 Sorted by residual: angle pdb=" CG SAH A 301 " pdb=" SD SAH A 301 " pdb=" C5' SAH A 301 " ideal model delta sigma weight residual 101.77 89.79 11.98 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O SAH A 301 " pdb=" C SAH A 301 " pdb=" OXT SAH A 301 " ideal model delta sigma weight residual 126.79 118.03 8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" C2 SAH A 301 " pdb=" N3 SAH A 301 " pdb=" C4 SAH A 301 " ideal model delta sigma weight residual 111.67 120.08 -8.41 3.00e+00 1.11e-01 7.86e+00 angle pdb=" N1 SAH A 301 " pdb=" C2 SAH A 301 " pdb=" N3 SAH A 301 " ideal model delta sigma weight residual 128.45 120.38 8.07 3.00e+00 1.11e-01 7.23e+00 angle pdb=" C5 SAH A 301 " pdb=" C4 SAH A 301 " pdb=" N3 SAH A 301 " ideal model delta sigma weight residual 126.55 120.38 6.17 3.00e+00 1.11e-01 4.23e+00 ... (remaining 8862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 3637 35.74 - 71.49: 181 71.49 - 107.23: 23 107.23 - 142.97: 0 142.97 - 178.72: 1 Dihedral angle restraints: 3842 sinusoidal: 2143 harmonic: 1699 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual -128.00 50.72 -178.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA TRP B 216 " pdb=" C TRP B 216 " pdb=" N GLU B 217 " pdb=" CA GLU B 217 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" O4' G C 44 " pdb=" C1' G C 44 " pdb=" N9 G C 44 " pdb=" C4 G C 44 " ideal model delta sinusoidal sigma weight residual -106.00 -158.27 52.27 1 1.70e+01 3.46e-03 1.29e+01 ... (remaining 3839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 728 0.027 - 0.054: 194 0.054 - 0.080: 51 0.080 - 0.107: 49 0.107 - 0.134: 17 Chirality restraints: 1039 Sorted by residual: chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" C3' SAH A 301 " pdb=" C2' SAH A 301 " pdb=" C4' SAH A 301 " pdb=" O3' SAH A 301 " both_signs ideal model delta sigma weight residual False -2.71 -2.58 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1036 not shown) Planarity restraints: 886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 59 " 0.029 2.00e-02 2.50e+03 1.27e-02 4.80e+00 pdb=" N9 G C 59 " -0.030 2.00e-02 2.50e+03 pdb=" C8 G C 59 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G C 59 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 59 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G C 59 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 59 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G C 59 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 59 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G C 59 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 253 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A C 43 " 0.017 2.00e-02 2.50e+03 7.65e-03 1.61e+00 pdb=" N9 A C 43 " -0.015 2.00e-02 2.50e+03 pdb=" C8 A C 43 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 43 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A C 43 " -0.006 2.00e-02 2.50e+03 pdb=" C6 A C 43 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A C 43 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A C 43 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A C 43 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A C 43 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A C 43 " -0.002 2.00e-02 2.50e+03 ... (remaining 883 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1421 2.80 - 3.32: 5474 3.32 - 3.85: 10987 3.85 - 4.37: 12762 4.37 - 4.90: 19964 Nonbonded interactions: 50608 Sorted by model distance: nonbonded pdb=" N2 G C 15 " pdb=" O2 C C 48 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR B 199 " pdb=" OE1 GLN B 200 " model vdw 2.270 3.040 nonbonded pdb=" N1 A C 14 " pdb=" O2' A C 21 " model vdw 2.278 3.120 nonbonded pdb=" O PRO B 201 " pdb=" OH TYR B 218 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP B 121 " pdb=" OG SER B 123 " model vdw 2.305 3.040 ... (remaining 50603 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=0.50 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: 0.170 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.002 0.057 6308 Z= 0.113 Angle : 0.486 11.983 8867 Z= 0.228 Chirality : 0.035 0.134 1039 Planarity : 0.003 0.034 886 Dihedral : 17.470 178.716 2744 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.36), residues: 573 helix: 3.40 (0.52), residues: 106 sheet: 1.24 (0.40), residues: 180 loop : 0.41 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 104 TYR 0.006 0.001 TYR A 195 PHE 0.012 0.001 PHE B 88 TRP 0.012 0.001 TRP B 216 HIS 0.002 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6308) covalent geometry : angle 0.48605 ( 8867) hydrogen bonds : bond 0.11553 ( 233) hydrogen bonds : angle 4.61712 ( 566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: B 147 MET cc_start: 0.8892 (ttt) cc_final: 0.8501 (ttp) REVERT: A 140 ASN cc_start: 0.9602 (t0) cc_final: 0.9248 (t0) REVERT: A 142 MET cc_start: 0.9605 (ttm) cc_final: 0.9374 (ttm) REVERT: A 147 ASN cc_start: 0.9579 (m110) cc_final: 0.9361 (m110) REVERT: A 234 LEU cc_start: 0.9436 (mt) cc_final: 0.8849 (tp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0704 time to fit residues: 5.2372 Evaluate side-chains 36 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.046084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.032838 restraints weight = 54216.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.034268 restraints weight = 21737.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.035250 restraints weight = 12870.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035875 restraints weight = 9272.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036313 restraints weight = 7544.361| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6308 Z= 0.186 Angle : 0.543 6.144 8867 Z= 0.269 Chirality : 0.038 0.175 1039 Planarity : 0.003 0.024 886 Dihedral : 20.732 177.065 1671 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.81 % Allowed : 8.10 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.36), residues: 573 helix: 3.59 (0.53), residues: 107 sheet: 1.02 (0.39), residues: 181 loop : 0.47 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 TYR 0.009 0.001 TYR B 371 PHE 0.011 0.001 PHE B 357 TRP 0.014 0.001 TRP B 216 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6308) covalent geometry : angle 0.54296 ( 8867) hydrogen bonds : bond 0.03985 ( 233) hydrogen bonds : angle 4.15007 ( 566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.196 Fit side-chains REVERT: B 147 MET cc_start: 0.8876 (ttt) cc_final: 0.8516 (ttp) REVERT: B 170 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8184 (ttp80) REVERT: A 140 ASN cc_start: 0.9560 (t0) cc_final: 0.9145 (t0) REVERT: A 147 ASN cc_start: 0.9643 (m110) cc_final: 0.9350 (m110) REVERT: A 234 LEU cc_start: 0.9495 (mt) cc_final: 0.9193 (tp) outliers start: 4 outliers final: 0 residues processed: 34 average time/residue: 0.0537 time to fit residues: 2.7574 Evaluate side-chains 28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.030018 restraints weight = 63314.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.031395 restraints weight = 23869.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032332 restraints weight = 13971.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.032890 restraints weight = 10075.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033319 restraints weight = 8268.043| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 6308 Z= 0.295 Angle : 0.654 5.818 8867 Z= 0.323 Chirality : 0.041 0.144 1039 Planarity : 0.003 0.021 886 Dihedral : 21.027 175.878 1671 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.01 % Allowed : 8.10 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.35), residues: 573 helix: 3.14 (0.52), residues: 108 sheet: 0.62 (0.38), residues: 183 loop : 0.21 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 138 TYR 0.008 0.001 TYR A 21 PHE 0.015 0.002 PHE B 288 TRP 0.013 0.002 TRP B 216 HIS 0.005 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00615 ( 6308) covalent geometry : angle 0.65397 ( 8867) hydrogen bonds : bond 0.04945 ( 233) hydrogen bonds : angle 4.51588 ( 566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.200 Fit side-chains REVERT: B 170 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.7879 (ttp80) REVERT: A 117 GLN cc_start: 0.9713 (mt0) cc_final: 0.9324 (mt0) REVERT: A 140 ASN cc_start: 0.9513 (t0) cc_final: 0.9287 (t0) REVERT: A 147 ASN cc_start: 0.9650 (m110) cc_final: 0.9365 (m110) outliers start: 5 outliers final: 1 residues processed: 32 average time/residue: 0.0639 time to fit residues: 3.1155 Evaluate side-chains 23 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031064 restraints weight = 79233.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032575 restraints weight = 25858.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033612 restraints weight = 14334.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.034308 restraints weight = 9947.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.034740 restraints weight = 7886.641| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6308 Z= 0.121 Angle : 0.504 6.674 8867 Z= 0.249 Chirality : 0.038 0.157 1039 Planarity : 0.003 0.025 886 Dihedral : 20.707 179.355 1671 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.61 % Allowed : 8.70 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.35), residues: 573 helix: 3.20 (0.52), residues: 108 sheet: 0.80 (0.38), residues: 182 loop : 0.21 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.006 0.001 TYR B 371 PHE 0.009 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6308) covalent geometry : angle 0.50397 ( 8867) hydrogen bonds : bond 0.03611 ( 233) hydrogen bonds : angle 3.96383 ( 566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 38 TYR cc_start: 0.8770 (t80) cc_final: 0.8520 (t80) REVERT: B 150 ASP cc_start: 0.8537 (t0) cc_final: 0.8160 (t0) REVERT: B 170 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8024 (ttp-170) REVERT: A 77 GLN cc_start: 0.9090 (pm20) cc_final: 0.8686 (mp10) REVERT: A 117 GLN cc_start: 0.9710 (mt0) cc_final: 0.9296 (mt0) REVERT: A 140 ASN cc_start: 0.9553 (t0) cc_final: 0.9273 (t0) REVERT: A 147 ASN cc_start: 0.9633 (m110) cc_final: 0.9380 (m110) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.0659 time to fit residues: 2.9181 Evaluate side-chains 26 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.029506 restraints weight = 78583.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.030912 restraints weight = 26449.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031908 restraints weight = 14899.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032513 restraints weight = 10449.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.032946 restraints weight = 8418.495| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6308 Z= 0.258 Angle : 0.593 6.508 8867 Z= 0.292 Chirality : 0.040 0.136 1039 Planarity : 0.003 0.025 886 Dihedral : 20.961 176.519 1671 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 9.11 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.36), residues: 573 helix: 3.22 (0.52), residues: 107 sheet: 0.64 (0.38), residues: 181 loop : 0.15 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.009 0.001 TYR B 38 PHE 0.011 0.001 PHE B 288 TRP 0.016 0.001 TRP B 216 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 6308) covalent geometry : angle 0.59291 ( 8867) hydrogen bonds : bond 0.04578 ( 233) hydrogen bonds : angle 4.27397 ( 566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8585 (t0) cc_final: 0.8176 (t0) REVERT: B 170 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8122 (ttp-170) REVERT: A 117 GLN cc_start: 0.9728 (mt0) cc_final: 0.9340 (mt0) REVERT: A 140 ASN cc_start: 0.9420 (t0) cc_final: 0.9182 (t0) REVERT: A 147 ASN cc_start: 0.9634 (m110) cc_final: 0.9349 (m110) outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 0.0670 time to fit residues: 3.0177 Evaluate side-chains 28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 180 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.030192 restraints weight = 53630.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.031465 restraints weight = 21582.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032350 restraints weight = 12873.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.032902 restraints weight = 9292.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.033230 restraints weight = 7584.764| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6308 Z= 0.205 Angle : 0.548 9.203 8867 Z= 0.268 Chirality : 0.039 0.139 1039 Planarity : 0.003 0.024 886 Dihedral : 20.872 178.681 1671 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.21 % Allowed : 9.11 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.36), residues: 573 helix: 3.23 (0.51), residues: 107 sheet: 0.78 (0.37), residues: 185 loop : 0.09 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.007 0.001 TYR A 195 PHE 0.010 0.001 PHE B 22 TRP 0.014 0.001 TRP B 216 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6308) covalent geometry : angle 0.54835 ( 8867) hydrogen bonds : bond 0.04055 ( 233) hydrogen bonds : angle 4.09036 ( 566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8520 (t0) cc_final: 0.8124 (t0) REVERT: B 170 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.7865 (ttp80) REVERT: A 117 GLN cc_start: 0.9719 (mt0) cc_final: 0.9325 (mt0) REVERT: A 140 ASN cc_start: 0.9387 (t0) cc_final: 0.9172 (t0) REVERT: A 147 ASN cc_start: 0.9638 (m110) cc_final: 0.9398 (m110) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.0636 time to fit residues: 3.0774 Evaluate side-chains 28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.043209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.031307 restraints weight = 51443.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.032560 restraints weight = 20552.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.033412 restraints weight = 12159.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033931 restraints weight = 8756.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034330 restraints weight = 7165.858| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6308 Z= 0.216 Angle : 0.569 8.492 8867 Z= 0.277 Chirality : 0.039 0.152 1039 Planarity : 0.003 0.024 886 Dihedral : 20.928 176.362 1671 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.81 % Allowed : 10.32 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.36), residues: 573 helix: 3.12 (0.51), residues: 108 sheet: 0.68 (0.37), residues: 187 loop : 0.08 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.009 0.001 TYR B 38 PHE 0.010 0.001 PHE B 22 TRP 0.015 0.001 TRP B 216 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6308) covalent geometry : angle 0.56906 ( 8867) hydrogen bonds : bond 0.04371 ( 233) hydrogen bonds : angle 4.15544 ( 566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8553 (t0) cc_final: 0.8125 (t0) REVERT: B 170 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8099 (ttp-170) REVERT: A 117 GLN cc_start: 0.9718 (mt0) cc_final: 0.9318 (mt0) REVERT: A 147 ASN cc_start: 0.9643 (m110) cc_final: 0.9386 (m110) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.0647 time to fit residues: 2.8835 Evaluate side-chains 28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029309 restraints weight = 71600.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.030604 restraints weight = 24719.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.031390 restraints weight = 13961.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.032056 restraints weight = 10212.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.032435 restraints weight = 8022.334| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6308 Z= 0.263 Angle : 0.609 8.057 8867 Z= 0.298 Chirality : 0.041 0.150 1039 Planarity : 0.003 0.026 886 Dihedral : 21.078 174.387 1671 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.21 % Allowed : 9.92 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.36), residues: 573 helix: 3.15 (0.50), residues: 107 sheet: 0.49 (0.37), residues: 185 loop : -0.00 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.007 0.001 TYR B 38 PHE 0.010 0.001 PHE B 288 TRP 0.016 0.002 TRP B 216 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 6308) covalent geometry : angle 0.60874 ( 8867) hydrogen bonds : bond 0.04735 ( 233) hydrogen bonds : angle 4.32069 ( 566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8525 (t0) cc_final: 0.8192 (t0) REVERT: B 170 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7944 (ttp80) REVERT: A 117 GLN cc_start: 0.9702 (mt0) cc_final: 0.9476 (mt0) REVERT: A 147 ASN cc_start: 0.9628 (m110) cc_final: 0.9397 (m110) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.0563 time to fit residues: 2.3730 Evaluate side-chains 25 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain A residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.030830 restraints weight = 51892.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.032134 restraints weight = 21079.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.033009 restraints weight = 12613.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.033495 restraints weight = 9167.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.033909 restraints weight = 7644.061| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6308 Z= 0.121 Angle : 0.522 9.227 8867 Z= 0.253 Chirality : 0.039 0.212 1039 Planarity : 0.003 0.023 886 Dihedral : 20.734 177.378 1671 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.81 % Allowed : 10.73 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.36), residues: 573 helix: 3.25 (0.51), residues: 107 sheet: 0.96 (0.38), residues: 180 loop : 0.09 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.005 0.001 TYR B 371 PHE 0.007 0.001 PHE B 88 TRP 0.013 0.001 TRP B 216 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6308) covalent geometry : angle 0.52203 ( 8867) hydrogen bonds : bond 0.03760 ( 233) hydrogen bonds : angle 3.88918 ( 566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8483 (t0) cc_final: 0.8082 (t0) REVERT: B 170 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.7902 (ttp80) REVERT: A 117 GLN cc_start: 0.9688 (mt0) cc_final: 0.9445 (mt0) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.0632 time to fit residues: 2.7009 Evaluate side-chains 24 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 216 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 0.0470 chunk 1 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.043052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030424 restraints weight = 45311.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.031677 restraints weight = 19618.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.032525 restraints weight = 12083.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033045 restraints weight = 8963.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.033387 restraints weight = 7470.941| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6308 Z= 0.126 Angle : 0.522 9.095 8867 Z= 0.253 Chirality : 0.039 0.164 1039 Planarity : 0.003 0.023 886 Dihedral : 20.696 176.590 1671 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.40 % Allowed : 11.54 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.37), residues: 573 helix: 3.27 (0.51), residues: 107 sheet: 1.06 (0.39), residues: 180 loop : 0.13 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.005 0.001 TYR B 371 PHE 0.009 0.001 PHE B 22 TRP 0.015 0.001 TRP B 216 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6308) covalent geometry : angle 0.52232 ( 8867) hydrogen bonds : bond 0.03882 ( 233) hydrogen bonds : angle 3.83855 ( 566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.204 Fit side-chains REVERT: B 150 ASP cc_start: 0.8508 (t0) cc_final: 0.8119 (t0) REVERT: B 170 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.7901 (ttp80) REVERT: A 117 GLN cc_start: 0.9680 (mt0) cc_final: 0.9276 (mt0) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.0601 time to fit residues: 2.5623 Evaluate side-chains 25 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 0.0170 overall best weight: 0.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.031862 restraints weight = 75615.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.033344 restraints weight = 24717.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.034371 restraints weight = 13567.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.035049 restraints weight = 9390.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035368 restraints weight = 7458.607| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6308 Z= 0.085 Angle : 0.506 9.672 8867 Z= 0.242 Chirality : 0.038 0.162 1039 Planarity : 0.003 0.021 886 Dihedral : 20.486 178.273 1671 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.20 % Allowed : 11.74 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.37), residues: 573 helix: 3.20 (0.50), residues: 110 sheet: 1.14 (0.40), residues: 174 loop : 0.21 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.005 0.001 TYR A 184 PHE 0.007 0.001 PHE B 22 TRP 0.015 0.001 TRP B 216 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 6308) covalent geometry : angle 0.50644 ( 8867) hydrogen bonds : bond 0.03585 ( 233) hydrogen bonds : angle 3.65324 ( 566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1047.51 seconds wall clock time: 18 minutes 49.58 seconds (1129.58 seconds total)