Starting phenix.real_space_refine on Thu Jul 2 03:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eg0_28108/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eg0_28108/07_2026/8eg0_28108.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'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: 1.78, per 1000 atoms: 0.30 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: 0.51 Conformation dependent library (CDL) restraints added in 353.3 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: 1.01 Time building geometry restraints manager: 0.67 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: 3521 35.74 - 71.49: 58 71.49 - 107.23: 6 107.23 - 142.97: 0 142.97 - 178.72: 1 Dihedral angle restraints: 3586 sinusoidal: 1887 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 3583 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: 0.050 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.270 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- 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 : 0.002 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 : 11.732 178.716 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 0.00222 / 0.11 ( 6308) covalent geometry : angle 0.48605 / 0.23 ( 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 : 0.148 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: 0.0690 time to fit residues: 5.1786 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 : 0.133 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.046162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.032948 restraints weight = 54579.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.034394 restraints weight = 21969.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035383 restraints weight = 13035.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035989 restraints weight = 9388.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036426 restraints weight = 7684.417| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 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 = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6308 Z= 0.189 Angle : 0.538 5.944 8867 Z= 0.267 Chirality : 0.038 0.181 1039 Planarity : 0.003 0.022 886 Dihedral : 13.300 177.298 1415 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 1.83 (0.36), residues: 573 helix: 3.59 (0.53), residues: 107 sheet: 1.04 (0.39), residues: 181 loop : 0.48 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 277 TYR 0.008 0.001 TYR B 371 PHE 0.012 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/Z covalent geometry : bond 0.00389 / 0.19 ( 6308) covalent geometry : angle 0.53795 / 0.27 ( 8867) hydrogen bonds : bond 0.03964 / 2.58 ( 233) hydrogen bonds : angle 4.14578 / 2.72 ( 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 : 0.204 Fit side-chains REVERT: B 147 MET cc_start: 0.8873 (ttt) cc_final: 0.8511 (ttp) REVERT: B 170 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8229 (ttp80) REVERT: A 140 ASN cc_start: 0.9561 (t0) cc_final: 0.9145 (t0) REVERT: A 147 ASN cc_start: 0.9635 (m110) cc_final: 0.9348 (m110) REVERT: A 234 LEU cc_start: 0.9505 (mt) cc_final: 0.9229 (tp) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.0582 time to fit residues: 3.1055 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 : 0.196 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.044771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031632 restraints weight = 72609.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.033072 restraints weight = 24510.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034086 restraints weight = 13706.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034781 restraints weight = 9543.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035187 restraints weight = 7533.030| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2230 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= 0.170 Angle : 0.527 5.976 8867 Z= 0.259 Chirality : 0.038 0.140 1039 Planarity : 0.003 0.019 886 Dihedral : 13.347 178.311 1415 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.81 % Allowed : 8.30 % 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: 1.68 (0.36), residues: 573 helix: 3.51 (0.52), residues: 107 sheet: 0.94 (0.39), residues: 181 loop : 0.38 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.005 0.001 TYR B 371 PHE 0.009 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 6308) covalent geometry : angle 0.52694 / 0.26 ( 8867) hydrogen bonds : bond 0.03834 / 2.56 ( 233) hydrogen bonds : angle 4.01594 / 2.63 ( 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: 4 poor density : 27 time to evaluate : 0.199 Fit side-chains REVERT: B 147 MET cc_start: 0.8819 (ttt) cc_final: 0.8528 (ttp) REVERT: B 170 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8112 (ttp-170) REVERT: A 140 ASN cc_start: 0.9568 (t0) cc_final: 0.9230 (t0) REVERT: A 147 ASN cc_start: 0.9659 (m110) cc_final: 0.9382 (m110) REVERT: A 234 LEU cc_start: 0.9499 (mt) cc_final: 0.9262 (tp) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.0619 time to fit residues: 2.8623 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 : 0.206 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.7342 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.045981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.032270 restraints weight = 88888.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.033847 restraints weight = 27242.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034968 restraints weight = 14732.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035680 restraints weight = 10088.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036164 restraints weight = 7959.722| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6308 Z= 0.105 Angle : 0.467 6.178 8867 Z= 0.232 Chirality : 0.037 0.160 1039 Planarity : 0.003 0.025 886 Dihedral : 13.232 179.207 1415 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.61 % Allowed : 8.30 % 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: 1.68 (0.36), residues: 573 helix: 3.42 (0.52), residues: 107 sheet: 1.21 (0.39), residues: 174 loop : 0.22 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 138 TYR 0.006 0.001 TYR B 371 PHE 0.010 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 6308) covalent geometry : angle 0.46678 / 0.23 ( 8867) hydrogen bonds : bond 0.03516 / 2.44 ( 233) hydrogen bonds : angle 3.76721 / 2.46 ( 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 : 0.154 Fit side-chains REVERT: B 38 TYR cc_start: 0.8879 (t80) cc_final: 0.8643 (t80) REVERT: B 147 MET cc_start: 0.8808 (ttt) cc_final: 0.8541 (ttp) REVERT: B 150 ASP cc_start: 0.8491 (t0) cc_final: 0.8003 (t0) REVERT: B 170 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8124 (ttp-170) REVERT: A 140 ASN cc_start: 0.9627 (t0) cc_final: 0.9298 (t0) REVERT: A 147 ASN cc_start: 0.9619 (m110) cc_final: 0.9370 (m110) REVERT: A 197 ILE cc_start: 0.9467 (tt) cc_final: 0.9205 (pt) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.0602 time to fit residues: 2.6722 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 : 0.215 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.045321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031733 restraints weight = 88263.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.033282 restraints weight = 26822.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034380 restraints weight = 14472.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.035073 restraints weight = 9893.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035547 restraints weight = 7808.782| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 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: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6308 Z= 0.123 Angle : 0.480 6.098 8867 Z= 0.236 Chirality : 0.037 0.143 1039 Planarity : 0.002 0.022 886 Dihedral : 13.269 178.741 1415 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.01 % Allowed : 8.50 % Favored : 90.49 % 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: 1.69 (0.36), residues: 573 helix: 3.45 (0.52), residues: 107 sheet: 1.03 (0.39), residues: 180 loop : 0.35 (0.37), 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 0.010 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6308) covalent geometry : angle 0.47966 / 0.24 ( 8867) hydrogen bonds : bond 0.03754 / 2.60 ( 233) hydrogen bonds : angle 3.69143 / 2.42 ( 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 31 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.164 Fit side-chains REVERT: B 147 MET cc_start: 0.8841 (ttt) cc_final: 0.8562 (ttp) REVERT: B 150 ASP cc_start: 0.8454 (t0) cc_final: 0.7960 (t0) REVERT: B 170 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8152 (ttp-170) REVERT: A 140 ASN cc_start: 0.9559 (t0) cc_final: 0.9231 (t0) REVERT: A 147 ASN cc_start: 0.9622 (m110) cc_final: 0.9389 (m110) REVERT: A 255 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9340 (mm) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 0.0514 time to fit residues: 2.4568 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 : 0.172 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3093 r_free = 0.3093 target = 0.044460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.031554 restraints weight = 56177.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.032927 restraints weight = 21926.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.033879 restraints weight = 12883.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.034501 restraints weight = 9248.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034878 restraints weight = 7499.918| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 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 = 0.2719 r_free = 0.2719 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: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2967 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= 0.151 Angle : 0.499 8.000 8867 Z= 0.245 Chirality : 0.037 0.142 1039 Planarity : 0.003 0.022 886 Dihedral : 13.379 179.065 1415 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 1.66 (0.36), residues: 573 helix: 3.43 (0.52), residues: 107 sheet: 1.10 (0.39), residues: 175 loop : 0.27 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.032 0.001 TYR B 38 PHE 0.011 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6308) covalent geometry : angle 0.49904 / 0.25 ( 8867) hydrogen bonds : bond 0.03942 / 2.74 ( 233) hydrogen bonds : angle 3.73775 / 2.44 ( 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: 6 poor density : 27 time to evaluate : 0.212 Fit side-chains REVERT: B 147 MET cc_start: 0.8847 (ttt) cc_final: 0.8549 (ttp) REVERT: B 150 ASP cc_start: 0.8511 (t0) cc_final: 0.8010 (t0) REVERT: B 170 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.7875 (ttp80) REVERT: A 117 GLN cc_start: 0.9705 (mt0) cc_final: 0.9294 (mt0) REVERT: A 140 ASN cc_start: 0.9487 (t0) cc_final: 0.9240 (t0) REVERT: A 147 ASN cc_start: 0.9635 (m110) cc_final: 0.9369 (m110) REVERT: A 255 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9330 (mm) outliers start: 6 outliers final: 0 residues processed: 33 average time/residue: 0.0533 time to fit residues: 2.6729 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 : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain A residue 255 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.043589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.030669 restraints weight = 51393.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.031977 restraints weight = 21281.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.032868 restraints weight = 12850.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033421 restraints weight = 9431.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.033723 restraints weight = 7787.955| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 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 = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6308 Z= 0.206 Angle : 0.559 7.879 8867 Z= 0.272 Chirality : 0.039 0.139 1039 Planarity : 0.003 0.021 886 Dihedral : 13.620 179.149 1415 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.81 % Allowed : 9.51 % 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: 1.53 (0.36), residues: 573 helix: 3.30 (0.52), residues: 108 sheet: 0.99 (0.38), residues: 186 loop : 0.17 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.010 0.001 TYR B 38 PHE 0.010 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 6308) covalent geometry : angle 0.55884 / 0.27 ( 8867) hydrogen bonds : bond 0.04360 / 2.99 ( 233) hydrogen bonds : angle 4.02901 / 2.62 ( 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 29 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.209 Fit side-chains REVERT: B 147 MET cc_start: 0.8868 (ttt) cc_final: 0.8581 (ttp) REVERT: B 150 ASP cc_start: 0.8514 (t0) cc_final: 0.8105 (t0) REVERT: B 170 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.7881 (ttp80) REVERT: A 117 GLN cc_start: 0.9718 (mt0) cc_final: 0.9327 (mt0) REVERT: A 140 ASN cc_start: 0.9437 (t0) cc_final: 0.9177 (t0) REVERT: A 147 ASN cc_start: 0.9641 (m110) cc_final: 0.9367 (m110) REVERT: A 255 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9306 (mm) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 0.0648 time to fit residues: 2.8276 Evaluate side-chains 27 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 255 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.042664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.029895 restraints weight = 70203.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031226 restraints weight = 24552.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032180 restraints weight = 13967.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.032805 restraints weight = 9824.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033203 restraints weight = 7830.738| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6308 Z= 0.225 Angle : 0.581 8.698 8867 Z= 0.281 Chirality : 0.040 0.138 1039 Planarity : 0.003 0.023 886 Dihedral : 13.841 179.678 1415 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.81 % Allowed : 9.92 % 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: 1.39 (0.36), residues: 573 helix: 3.31 (0.51), residues: 107 sheet: 0.80 (0.38), residues: 188 loop : 0.12 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.010 0.001 TYR B 38 PHE 0.012 0.001 PHE B 22 TRP 0.013 0.001 TRP B 216 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 ( 6308) covalent geometry : angle 0.58140 / 0.28 ( 8867) hydrogen bonds : bond 0.04513 / 3.12 ( 233) hydrogen bonds : angle 4.07620 / 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 28 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8525 (t0) cc_final: 0.8178 (t0) REVERT: B 170 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: A 117 GLN cc_start: 0.9712 (mt0) cc_final: 0.9326 (mt0) REVERT: A 147 ASN cc_start: 0.9621 (m110) cc_final: 0.9405 (m110) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.0654 time to fit residues: 2.7848 Evaluate side-chains 24 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.043746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031120 restraints weight = 49959.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.032408 restraints weight = 20773.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.033281 restraints weight = 12527.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.033805 restraints weight = 9188.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.034181 restraints weight = 7626.069| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3707 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= 0.148 Angle : 0.534 9.086 8867 Z= 0.256 Chirality : 0.038 0.140 1039 Planarity : 0.003 0.020 886 Dihedral : 13.583 179.805 1415 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.61 % Allowed : 10.53 % 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: 1.51 (0.36), residues: 573 helix: 3.32 (0.51), residues: 107 sheet: 0.93 (0.38), residues: 185 loop : 0.20 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.005 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 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 6308) covalent geometry : angle 0.53401 / 0.26 ( 8867) hydrogen bonds : bond 0.04023 / 2.84 ( 233) hydrogen bonds : angle 3.88573 / 2.52 ( 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 30 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.8474 (t0) cc_final: 0.8185 (t0) REVERT: B 170 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7883 (ttp80) REVERT: A 117 GLN cc_start: 0.9684 (mt0) cc_final: 0.9275 (mt0) REVERT: A 147 ASN cc_start: 0.9619 (m110) cc_final: 0.9362 (m110) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.0592 time to fit residues: 2.6442 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE 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 41 optimal weight: 0.0470 chunk 1 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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 = 0.3107 r_free = 0.3107 target = 0.044867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.031898 restraints weight = 56158.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.033285 restraints weight = 21607.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.034227 restraints weight = 12612.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034802 restraints weight = 9071.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035154 restraints weight = 7400.496| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6308 Z= 0.093 Angle : 0.510 9.712 8867 Z= 0.243 Chirality : 0.038 0.214 1039 Planarity : 0.003 0.021 886 Dihedral : 13.275 179.054 1415 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.61 % Allowed : 10.53 % 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: 1.64 (0.36), residues: 573 helix: 3.31 (0.51), residues: 107 sheet: 1.17 (0.38), residues: 181 loop : 0.22 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.005 0.001 TYR B 371 PHE 0.009 0.001 PHE B 22 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 0.00202 / 0.09 ( 6308) covalent geometry : angle 0.51018 / 0.24 ( 8867) hydrogen bonds : bond 0.03656 / 2.65 ( 233) hydrogen bonds : angle 3.65224 / 2.38 ( 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 33 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.203 Fit side-chains REVERT: B 147 MET cc_start: 0.8895 (ttt) cc_final: 0.8598 (ttp) REVERT: B 150 ASP cc_start: 0.8585 (t0) cc_final: 0.7993 (t0) REVERT: B 170 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7938 (ttp80) REVERT: A 117 GLN cc_start: 0.9674 (mt0) cc_final: 0.9196 (mt0) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.0495 time to fit residues: 2.5490 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 : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE 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: 8.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.047696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.034598 restraints weight = 87452.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.036179 restraints weight = 28061.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037265 restraints weight = 15268.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037946 restraints weight = 10536.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.038403 restraints weight = 8352.354| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6308 Z= 0.088 Angle : 0.523 9.728 8867 Z= 0.248 Chirality : 0.038 0.178 1039 Planarity : 0.003 0.020 886 Dihedral : 13.192 179.805 1415 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.40 % Allowed : 11.34 % Favored : 88.26 % 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: 1.69 (0.36), residues: 573 helix: 3.20 (0.51), residues: 107 sheet: 1.36 (0.39), residues: 181 loop : 0.19 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.006 0.001 TYR B 38 PHE 0.009 0.001 PHE B 22 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 0.00198 / 0.09 ( 6308) covalent geometry : angle 0.52259 / 0.25 ( 8867) hydrogen bonds : bond 0.03645 / 2.65 ( 233) hydrogen bonds : angle 3.55881 / 2.32 ( 566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.73 seconds wall clock time: 18 minutes 18.92 seconds (1098.92 seconds total)