Starting phenix.real_space_refine on Tue Aug 4 19:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eg0_28108/08_2026/8eg0_28108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eg0_28108/08_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_28108/08_2026/8eg0_28108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eg0_28108/08_2026/8eg0_28108.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eg0_28108/08_2026/8eg0_28108.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eg0_28108/08_2026/8eg0_28108.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eg0_28108/08_2026/8eg0_28108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eg0_28108/08_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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 1.35, per 1000 atoms: 0.22 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: 0.53 Conformation dependent library (CDL) restraints added in 363.3 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: 0.73 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: 1.19 Time building geometry restraints manager: 0.73 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: 8640 2.40 - 4.79: 212 4.79 - 7.19: 11 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=" O3' A C 58 " pdb=" C3' A C 58 " pdb=" C2' A C 58 " ideal model delta sigma weight residual 113.80 108.66 5.14 2.00e+00 2.50e-01 6.60e+00 ... (remaining 8862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 3233 15.80 - 31.59: 173 31.59 - 47.38: 96 47.38 - 63.18: 68 63.18 - 78.97: 16 Dihedral angle restraints: 3586 sinusoidal: 1887 harmonic: 1699 Sorted by residual: dihedral pdb=" C4' A C 58 " pdb=" C3' A C 58 " pdb=" C2' A C 58 " pdb=" C1' A C 58 " ideal model delta sinusoidal sigma weight residual 36.34 -36.47 72.81 1 3.10e+00 1.04e-01 7.04e+02 dihedral pdb=" C4' G C 45 " pdb=" C3' G C 45 " pdb=" C2' G C 45 " pdb=" C1' G C 45 " ideal model delta sinusoidal sigma weight residual 36.34 -36.01 72.36 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' C C 48 " pdb=" C3' C C 48 " pdb=" C2' C C 48 " pdb=" C1' C C 48 " ideal model delta sinusoidal sigma weight residual 36.34 -35.89 72.23 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 3583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 848 0.058 - 0.115: 96 0.115 - 0.173: 4 0.173 - 0.231: 31 0.231 - 0.289: 60 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C2' G C 44 " pdb=" C3' G C 44 " pdb=" O2' G C 44 " pdb=" C1' G C 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' A C 58 " pdb=" C4' A C 58 " pdb=" O3' A C 58 " pdb=" C2' A C 58 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G C 18 " pdb=" C3' G C 18 " pdb=" O2' G C 18 " pdb=" C1' G C 18 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (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: 0.230 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.730 Find NCS groups from input model: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.003 0.057 6308 Z= 0.128 Angle : 0.682 11.983 8867 Z= 0.291 Chirality : 0.080 0.289 1039 Planarity : 0.003 0.034 886 Dihedral : 15.341 78.973 2488 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/Z covalent geometry : bond 0.00256 / 0.13 ( 6308) covalent geometry : angle 0.68172 / 0.29 ( 8867) hydrogen bonds : bond 0.11553 / 8.12 ( 233) hydrogen bonds : angle 4.61712 / 3.03 ( 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 : 0.205 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: 0.0715 time to fit residues: 5.4238 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 : 0.204 ------------------------------------------------------------------------------- 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... B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.033188 restraints weight = 56256.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034665 restraints weight = 22336.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035673 restraints weight = 13126.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036302 restraints weight = 9400.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036733 restraints weight = 7636.893| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6308 Z= 0.218 Angle : 0.962 13.167 8867 Z= 0.404 Chirality : 0.077 0.622 1039 Planarity : 0.003 0.021 886 Dihedral : 16.799 151.699 1415 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.61 % Allowed : 7.89 % Favored : 91.50 % 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: 1.78 (0.36), residues: 573 helix: 3.57 (0.53), residues: 108 sheet: 1.10 (0.40), residues: 179 loop : 0.37 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 170 TYR 0.006 0.001 TYR B 371 PHE 0.011 0.001 PHE B 357 TRP 0.014 0.001 TRP B 216 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 ( 6308) covalent geometry : angle 0.96223 / 0.40 ( 8867) hydrogen bonds : bond 0.05293 / 3.78 ( 233) hydrogen bonds : angle 4.17485 / 2.74 ( 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: 3 poor density : 32 time to evaluate : 0.206 Fit side-chains REVERT: B 147 MET cc_start: 0.8894 (ttt) cc_final: 0.8584 (ttp) REVERT: B 170 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: A 77 GLN cc_start: 0.8940 (pm20) cc_final: 0.8736 (mp-120) REVERT: A 140 ASN cc_start: 0.9567 (t0) cc_final: 0.9134 (t0) REVERT: A 147 ASN cc_start: 0.9631 (m110) cc_final: 0.9348 (m110) REVERT: A 234 LEU cc_start: 0.9486 (mt) cc_final: 0.9190 (tp) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.0627 time to fit residues: 3.2525 Evaluate side-chains 30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031104 restraints weight = 69409.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.032528 restraints weight = 24639.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033529 restraints weight = 14025.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.034191 restraints weight = 9893.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.034491 restraints weight = 7929.951| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6308 Z= 0.246 Angle : 0.841 9.469 8867 Z= 0.366 Chirality : 0.064 0.564 1039 Planarity : 0.003 0.022 886 Dihedral : 17.034 164.818 1415 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.61 % Allowed : 9.31 % Favored : 90.08 % 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: 1.52 (0.36), residues: 573 helix: 3.42 (0.52), residues: 107 sheet: 0.77 (0.39), residues: 183 loop : 0.29 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 24 TYR 0.007 0.001 TYR A 37 PHE 0.012 0.001 PHE B 288 TRP 0.014 0.001 TRP B 216 HIS 0.006 0.002 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.25 ( 6308) covalent geometry : angle 0.84066 / 0.37 ( 8867) hydrogen bonds : bond 0.05093 / 3.47 ( 233) hydrogen bonds : angle 4.26969 / 2.79 ( 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 31 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.208 Fit side-chains REVERT: B 147 MET cc_start: 0.8810 (ttt) cc_final: 0.8511 (ttp) REVERT: B 170 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8043 (ttp-170) REVERT: A 140 ASN cc_start: 0.9471 (t0) cc_final: 0.9191 (t0) REVERT: A 147 ASN cc_start: 0.9647 (m110) cc_final: 0.9378 (m110) REVERT: A 234 LEU cc_start: 0.9528 (mt) cc_final: 0.9306 (tp) outliers start: 3 outliers final: 0 residues processed: 31 average time/residue: 0.0651 time to fit residues: 3.0868 Evaluate side-chains 26 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.045374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031847 restraints weight = 80742.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033332 restraints weight = 25926.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.034406 restraints weight = 14289.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.035107 restraints weight = 9823.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035519 restraints weight = 7748.800| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6308 Z= 0.153 Angle : 0.734 8.754 8867 Z= 0.316 Chirality : 0.060 0.563 1039 Planarity : 0.003 0.017 886 Dihedral : 16.936 162.954 1415 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.21 % Allowed : 8.10 % 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: 1.52 (0.36), residues: 573 helix: 3.36 (0.52), residues: 107 sheet: 0.80 (0.38), residues: 183 loop : 0.31 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.008 0.001 TYR B 38 PHE 0.010 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6308) covalent geometry : angle 0.73436 / 0.32 ( 8867) hydrogen bonds : bond 0.04363 / 3.19 ( 233) hydrogen bonds : angle 3.91720 / 2.55 ( 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 35 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.210 Fit side-chains REVERT: B 147 MET cc_start: 0.8786 (ttt) cc_final: 0.8507 (ttm) REVERT: B 150 ASP cc_start: 0.8508 (t0) cc_final: 0.8152 (t0) REVERT: B 170 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8014 (ttp-170) REVERT: A 77 GLN cc_start: 0.9151 (pm20) cc_final: 0.8770 (mp10) REVERT: A 140 ASN cc_start: 0.9494 (t0) cc_final: 0.9223 (t0) REVERT: A 147 ASN cc_start: 0.9625 (m110) cc_final: 0.9367 (m110) REVERT: A 255 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9341 (mm) outliers start: 6 outliers final: 2 residues processed: 35 average time/residue: 0.0614 time to fit residues: 3.3238 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.044505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.031188 restraints weight = 83308.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.032664 restraints weight = 25928.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.033725 restraints weight = 14058.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.034381 restraints weight = 9644.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034843 restraints weight = 7643.526| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3461 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= 0.188 Angle : 0.754 7.710 8867 Z= 0.325 Chirality : 0.059 0.570 1039 Planarity : 0.003 0.017 886 Dihedral : 16.881 161.962 1415 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.42 % Allowed : 8.30 % Favored : 90.28 % 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 (0.36), residues: 573 helix: 3.34 (0.52), residues: 107 sheet: 0.82 (0.39), residues: 181 loop : 0.28 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.008 0.001 TYR B 38 PHE 0.011 0.001 PHE B 22 TRP 0.014 0.001 TRP B 216 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 ( 6308) covalent geometry : angle 0.75413 / 0.32 ( 8867) hydrogen bonds : bond 0.04682 / 3.33 ( 233) hydrogen bonds : angle 3.95274 / 2.58 ( 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 34 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8604 (t0) cc_final: 0.7980 (t0) REVERT: B 170 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8113 (ttp-170) REVERT: A 117 GLN cc_start: 0.9708 (mt0) cc_final: 0.9301 (mt0) REVERT: A 140 ASN cc_start: 0.9433 (t0) cc_final: 0.9221 (t0) REVERT: A 147 ASN cc_start: 0.9619 (m110) cc_final: 0.9364 (m110) REVERT: A 255 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9376 (mm) outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.0642 time to fit residues: 3.1615 Evaluate side-chains 31 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 30 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.030738 restraints weight = 53711.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032028 restraints weight = 21238.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.032935 restraints weight = 12579.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.033495 restraints weight = 9077.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.033858 restraints weight = 7443.078| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6308 Z= 0.240 Angle : 0.802 9.603 8867 Z= 0.347 Chirality : 0.060 0.605 1039 Planarity : 0.003 0.019 886 Dihedral : 16.968 162.239 1415 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.42 % Allowed : 9.31 % Favored : 89.27 % 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: 1.22 (0.36), residues: 573 helix: 3.17 (0.52), residues: 108 sheet: 0.68 (0.38), residues: 180 loop : 0.02 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.009 0.001 TYR B 38 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/Z covalent geometry : bond 0.00510 / 0.24 ( 6308) covalent geometry : angle 0.80226 / 0.35 ( 8867) hydrogen bonds : bond 0.04960 / 3.51 ( 233) hydrogen bonds : angle 4.16394 / 2.70 ( 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 33 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8647 (t0) cc_final: 0.8092 (t0) REVERT: B 170 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: A 117 GLN cc_start: 0.9719 (mt0) cc_final: 0.9334 (mt0) REVERT: A 140 ASN cc_start: 0.9381 (t0) cc_final: 0.9175 (t0) REVERT: A 147 ASN cc_start: 0.9636 (m110) cc_final: 0.9361 (m110) outliers start: 7 outliers final: 2 residues processed: 32 average time/residue: 0.0610 time to fit residues: 2.9982 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 : 0.177 ------------------------------------------------------------------------------- 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 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.043970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.030894 restraints weight = 50598.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.032166 restraints weight = 20497.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.033044 restraints weight = 12328.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.033609 restraints weight = 9036.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.033955 restraints weight = 7438.427| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3953 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= 0.170 Angle : 0.749 8.925 8867 Z= 0.321 Chirality : 0.059 0.568 1039 Planarity : 0.003 0.018 886 Dihedral : 16.837 161.508 1415 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.81 % Allowed : 9.72 % Favored : 89.47 % 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: 1.38 (0.36), residues: 573 helix: 3.30 (0.51), residues: 107 sheet: 0.83 (0.38), residues: 186 loop : 0.08 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.006 0.001 TYR B 38 PHE 0.008 0.001 PHE A 159 TRP 0.013 0.001 TRP B 216 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 6308) covalent geometry : angle 0.74879 / 0.32 ( 8867) hydrogen bonds : bond 0.04548 / 3.32 ( 233) hydrogen bonds : angle 3.98194 / 2.58 ( 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 31 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8621 (t0) cc_final: 0.8000 (t0) REVERT: B 170 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7974 (ttp80) REVERT: A 117 GLN cc_start: 0.9708 (mt0) cc_final: 0.9307 (mt0) REVERT: A 147 ASN cc_start: 0.9627 (m110) cc_final: 0.9374 (m110) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.0635 time to fit residues: 2.9043 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 : 0.204 ------------------------------------------------------------------------------- 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 30 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.032663 restraints weight = 81341.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.034108 restraints weight = 27457.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.035139 restraints weight = 15343.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.035807 restraints weight = 10675.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.036169 restraints weight = 8536.611| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 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 = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6308 Z= 0.214 Angle : 0.779 8.493 8867 Z= 0.336 Chirality : 0.059 0.580 1039 Planarity : 0.003 0.018 886 Dihedral : 16.859 161.183 1415 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 1.30 (0.36), residues: 573 helix: 3.25 (0.51), residues: 107 sheet: 0.72 (0.38), residues: 186 loop : 0.07 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.010 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 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 ( 6308) covalent geometry : angle 0.77930 / 0.34 ( 8867) hydrogen bonds : bond 0.04928 / 3.54 ( 233) hydrogen bonds : angle 4.06759 / 2.64 ( 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 30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8636 (t0) cc_final: 0.8158 (t0) REVERT: B 170 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: A 117 GLN cc_start: 0.9713 (mt0) cc_final: 0.9325 (mt0) REVERT: A 147 ASN cc_start: 0.9599 (m110) cc_final: 0.9347 (m110) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0652 time to fit residues: 2.8242 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 : 0.184 ------------------------------------------------------------------------------- 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 30 MET Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.029251 restraints weight = 47299.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.030422 restraints weight = 20476.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031209 restraints weight = 12587.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.031744 restraints weight = 9276.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032082 restraints weight = 7616.228| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 6308 Z= 0.391 Angle : 0.948 9.694 8867 Z= 0.414 Chirality : 0.064 0.633 1039 Planarity : 0.004 0.027 886 Dihedral : 17.221 165.053 1415 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.21 % Allowed : 10.12 % Favored : 88.66 % 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: 0.74 (0.35), residues: 573 helix: 2.85 (0.49), residues: 108 sheet: 0.29 (0.38), residues: 186 loop : -0.26 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 246 TYR 0.013 0.002 TYR B 38 PHE 0.013 0.002 PHE A 159 TRP 0.016 0.002 TRP B 216 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.39 ( 6308) covalent geometry : angle 0.94813 / 0.41 ( 8867) hydrogen bonds : bond 0.06249 / 4.35 ( 233) hydrogen bonds : angle 4.69291 / 3.04 ( 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 26 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.196 Fit side-chains REVERT: B 170 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: A 117 GLN cc_start: 0.9729 (mt0) cc_final: 0.9522 (mt0) REVERT: A 147 ASN cc_start: 0.9619 (m110) cc_final: 0.9379 (m110) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.0564 time to fit residues: 2.1526 Evaluate side-chains 24 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031466 restraints weight = 42298.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.032652 restraints weight = 18484.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.033513 restraints weight = 11499.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.034052 restraints weight = 8421.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.034423 restraints weight = 6947.450| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6308 Z= 0.129 Angle : 0.763 9.381 8867 Z= 0.329 Chirality : 0.061 0.576 1039 Planarity : 0.003 0.021 886 Dihedral : 16.857 164.846 1415 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.40 % Allowed : 11.13 % 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: 1.17 (0.36), residues: 573 helix: 3.13 (0.49), residues: 107 sheet: 0.64 (0.39), residues: 176 loop : 0.02 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.007 0.001 TYR B 371 PHE 0.008 0.001 PHE B 190 TRP 0.014 0.001 TRP B 216 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 6308) covalent geometry : angle 0.76306 / 0.33 ( 8867) hydrogen bonds : bond 0.04380 / 3.26 ( 233) hydrogen bonds : angle 4.01799 / 2.61 ( 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 : 0.119 Fit side-chains REVERT: B 147 MET cc_start: 0.8174 (ptp) cc_final: 0.7639 (mtt) REVERT: B 150 ASP cc_start: 0.8538 (t0) cc_final: 0.8127 (t0) REVERT: B 170 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.7944 (ttp80) REVERT: A 117 GLN cc_start: 0.9676 (mt0) cc_final: 0.9423 (mt0) REVERT: A 147 ASN cc_start: 0.9632 (m110) cc_final: 0.9429 (m110) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.0421 time to fit residues: 1.7567 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.032500 restraints weight = 78997.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.033983 restraints weight = 24907.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035030 restraints weight = 13553.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035717 restraints weight = 9346.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036127 restraints weight = 7412.877| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6308 Z= 0.109 Angle : 0.717 9.577 8867 Z= 0.306 Chirality : 0.058 0.510 1039 Planarity : 0.003 0.019 886 Dihedral : 16.512 159.604 1415 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.40 % Allowed : 11.13 % 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: 1.48 (0.37), residues: 573 helix: 3.06 (0.51), residues: 107 sheet: 1.26 (0.39), residues: 182 loop : 0.01 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.009 0.001 TYR A 184 PHE 0.009 0.001 PHE A 159 TRP 0.014 0.001 TRP B 216 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6308) covalent geometry : angle 0.71741 / 0.31 ( 8867) hydrogen bonds : bond 0.04276 / 3.19 ( 233) hydrogen bonds : angle 3.63601 / 2.37 ( 566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.93 seconds wall clock time: 19 minutes 0.51 seconds (1140.51 seconds total)