Starting phenix.real_space_refine on Thu Jul 2 06:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umc_42375/07_2026/8umc_42375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umc_42375/07_2026/8umc_42375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umc_42375/07_2026/8umc_42375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umc_42375/07_2026/8umc_42375.map" model { file = "/net/cci-nas-00/data/ceres_data/8umc_42375/07_2026/8umc_42375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umc_42375/07_2026/8umc_42375.cif" } resolution = 2.5 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= 0.001 sd= 0.021 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 Mn 2 7.51 5 S 54 5.16 5 C 4564 2.51 5 N 1270 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s 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: 7198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2630 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 968 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2630 Classifications: {'peptide': 322} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 968 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.16 Number of scatterers: 7198 At special positions: 0 Unit cell: (107.06, 80.8, 82.82, 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) Mn 2 24.99 S 54 16.00 O 1308 8.00 N 1270 7.00 C 4564 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: 0.45 Conformation dependent library (CDL) restraints added in 246.9 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 43.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.563A pdb=" N GLU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.770A pdb=" N ARG A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.860A pdb=" N THR A 180 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.030A pdb=" N LEU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 309 through 325 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.367A pdb=" N ASP B 68 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.658A pdb=" N TYR C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 111 removed outlier: 3.659A pdb=" N ASP C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.685A pdb=" N SER C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.996A pdb=" N LEU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.526A pdb=" N GLU C 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 309 through 325 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.093A pdb=" N ILE A 115 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A 143 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 117 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 114 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 75 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ARG A 116 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS A 77 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 41 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS A 77 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A 43 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 40 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 7 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER A 294 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY A 9 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TYR A 296 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N SER A 11 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 258 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 295 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 260 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48 removed outlier: 4.707A pdb=" N VAL B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 94 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.707A pdb=" N LEU C 140 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 173 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 142 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 115 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 143 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 117 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 41 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N HIS C 77 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER C 43 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 40 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 7 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER C 294 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 9 " --> pdb=" O SER C 294 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N TYR C 296 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER C 11 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.543A pdb=" N THR D 84 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32 Processing sheet with id=AA9, first strand: chain 'D' and resid 46 through 47 removed outlier: 3.529A pdb=" N GLU D 46 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 43 " --> pdb=" O GLU D 46 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.63 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: 2438 1.34 - 1.46: 1331 1.46 - 1.57: 3499 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 7368 Sorted by residual: bond pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.76e+00 bond pdb=" N ASP A 266 " pdb=" CA ASP A 266 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.34e-02 5.57e+03 7.07e+00 bond pdb=" N GLN C 268 " pdb=" CA GLN C 268 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.18e-02 7.18e+03 6.98e+00 bond pdb=" N HIS A 145 " pdb=" CA HIS A 145 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.18e-02 7.18e+03 6.86e+00 ... (remaining 7363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 9339 1.26 - 2.53: 487 2.53 - 3.79: 104 3.79 - 5.05: 21 5.05 - 6.32: 3 Bond angle restraints: 9954 Sorted by residual: angle pdb=" N PRO A 147 " pdb=" CA PRO A 147 " pdb=" CB PRO A 147 " ideal model delta sigma weight residual 103.25 96.93 6.32 1.05e+00 9.07e-01 3.62e+01 angle pdb=" CA ILE A 302 " pdb=" C ILE A 302 " pdb=" O ILE A 302 " ideal model delta sigma weight residual 122.63 118.54 4.09 8.70e-01 1.32e+00 2.21e+01 angle pdb=" N MET C 320 " pdb=" CA MET C 320 " pdb=" C MET C 320 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.20e+01 angle pdb=" CA ASP C 266 " pdb=" C ASP C 266 " pdb=" O ASP C 266 " ideal model delta sigma weight residual 122.01 118.23 3.78 1.05e+00 9.07e-01 1.30e+01 angle pdb=" CA ASP A 266 " pdb=" C ASP A 266 " pdb=" O ASP A 266 " ideal model delta sigma weight residual 122.01 118.28 3.73 1.05e+00 9.07e-01 1.26e+01 ... (remaining 9949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 4078 26.28 - 52.56: 288 52.56 - 78.84: 47 78.84 - 105.12: 10 105.12 - 131.40: 1 Dihedral angle restraints: 4424 sinusoidal: 1862 harmonic: 2562 Sorted by residual: dihedral pdb=" CA ALA A 146 " pdb=" C ALA A 146 " pdb=" N PRO A 147 " pdb=" CA PRO A 147 " ideal model delta harmonic sigma weight residual 180.00 48.60 131.40 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CA ARG C 193 " pdb=" C ARG C 193 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ARG C 105 " pdb=" C ARG C 105 " pdb=" N HIS C 106 " pdb=" CA HIS C 106 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 801 0.049 - 0.098: 192 0.098 - 0.147: 55 0.147 - 0.197: 6 0.197 - 0.246: 2 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA MET C 320 " pdb=" N MET C 320 " pdb=" C MET C 320 " pdb=" CB MET C 320 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 15 " pdb=" N VAL B 15 " pdb=" C VAL B 15 " pdb=" CB VAL B 15 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 1053 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 210 " 0.313 9.50e-02 1.11e+02 1.40e-01 1.21e+01 pdb=" NE ARG A 210 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 210 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 210 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 210 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.56e+00 pdb=" NE ARG A 254 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " 0.178 9.50e-02 1.11e+02 7.99e-02 4.29e+00 pdb=" NE ARG A 270 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " 0.003 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 113 2.62 - 3.19: 6478 3.19 - 3.76: 11573 3.76 - 4.33: 17203 4.33 - 4.90: 27913 Nonbonded interactions: 63280 Sorted by model distance: nonbonded pdb=" OH TYR B 27 " pdb=" OH TYR B 108 " model vdw 2.045 3.040 nonbonded pdb=" OH TYR D 28 " pdb=" OH TYR D 108 " model vdw 2.048 3.040 nonbonded pdb=" OE1 GLU A 295 " pdb="MN MN A 401 " model vdw 2.101 3.060 nonbonded pdb=" OE1 GLU C 295 " pdb="MN MN C 401 " model vdw 2.115 3.060 nonbonded pdb=" O LYS C 261 " pdb=" OH TYR C 276 " model vdw 2.133 3.040 ... (remaining 63275 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.940 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7368 Z= 0.289 Angle : 0.683 6.318 9954 Z= 0.420 Chirality : 0.048 0.246 1056 Planarity : 0.007 0.140 1310 Dihedral : 17.532 131.399 2780 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.16 % Allowed : 19.51 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.80 (0.28), residues: 882 helix: 0.14 (0.28), residues: 344 sheet: -1.05 (0.42), residues: 154 loop : -0.79 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 270 TYR 0.014 0.001 TYR A 13 PHE 0.012 0.002 PHE C 20 TRP 0.007 0.001 TRP A 242 HIS 0.006 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.29 ( 7368) covalent geometry : angle 0.68272 / 0.42 ( 9954) hydrogen bonds : bond 0.15222 / 9.79 ( 305) hydrogen bonds : angle 6.77669 / 4.81 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 241 ASN cc_start: 0.8181 (p0) cc_final: 0.7918 (p0) outliers start: 9 outliers final: 5 residues processed: 221 average time/residue: 0.5008 time to fit residues: 115.7878 Evaluate side-chains 214 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain D residue 62 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.135170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125810 restraints weight = 9009.482| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.30 r_work: 0.3606 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7368 Z= 0.134 Angle : 0.557 5.167 9954 Z= 0.292 Chirality : 0.043 0.169 1056 Planarity : 0.005 0.054 1310 Dihedral : 5.462 64.589 1004 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.49 % Allowed : 19.77 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.21 (0.29), residues: 882 helix: 0.76 (0.29), residues: 334 sheet: -0.98 (0.43), residues: 154 loop : -0.44 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 270 TYR 0.013 0.001 TYR D 28 PHE 0.012 0.001 PHE A 150 TRP 0.006 0.001 TRP A 63 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7368) covalent geometry : angle 0.55748 / 0.29 ( 9954) hydrogen bonds : bond 0.03512 / 2.28 ( 305) hydrogen bonds : angle 5.40230 / 3.86 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8140 (mptt) cc_final: 0.7916 (mttp) REVERT: A 61 ASP cc_start: 0.7505 (m-30) cc_final: 0.7237 (m-30) REVERT: A 207 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8022 (mm110) REVERT: A 300 ARG cc_start: 0.8030 (ptp-170) cc_final: 0.7818 (ptp-170) REVERT: C 241 ASN cc_start: 0.8104 (p0) cc_final: 0.7873 (p0) REVERT: C 278 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: C 308 VAL cc_start: 0.8509 (t) cc_final: 0.8304 (p) outliers start: 27 outliers final: 13 residues processed: 231 average time/residue: 0.4787 time to fit residues: 116.0526 Evaluate side-chains 223 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 43 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 207 GLN A 241 ASN C 96 GLN C 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123300 restraints weight = 8916.998| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.30 r_work: 0.3577 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7368 Z= 0.193 Angle : 0.589 5.679 9954 Z= 0.306 Chirality : 0.045 0.165 1056 Planarity : 0.005 0.102 1310 Dihedral : 5.430 57.874 1000 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.13 % Allowed : 20.54 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.18 (0.29), residues: 882 helix: 0.78 (0.28), residues: 334 sheet: -1.16 (0.42), residues: 162 loop : -0.29 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 210 TYR 0.009 0.002 TYR D 5 PHE 0.015 0.002 PHE C 20 TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 7368) covalent geometry : angle 0.58876 / 0.31 ( 9954) hydrogen bonds : bond 0.03699 / 2.37 ( 305) hydrogen bonds : angle 5.21821 / 3.73 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8178 (mptt) cc_final: 0.7928 (mttp) REVERT: A 61 ASP cc_start: 0.7520 (m-30) cc_final: 0.7217 (m-30) REVERT: A 207 GLN cc_start: 0.8662 (mm110) cc_final: 0.8264 (mm110) REVERT: A 210 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7939 (mtm-85) REVERT: C 49 MET cc_start: 0.8544 (mtt) cc_final: 0.8181 (mtt) REVERT: C 203 TYR cc_start: 0.8242 (t80) cc_final: 0.7846 (t80) REVERT: C 232 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7967 (ttm110) REVERT: C 241 ASN cc_start: 0.8134 (p0) cc_final: 0.7894 (p0) REVERT: C 278 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: D 29 ARG cc_start: 0.8587 (ptt90) cc_final: 0.8341 (ptt-90) outliers start: 32 outliers final: 14 residues processed: 231 average time/residue: 0.4985 time to fit residues: 120.6181 Evaluate side-chains 221 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN C 96 GLN C 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123352 restraints weight = 9028.684| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.30 r_work: 0.3575 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7368 Z= 0.207 Angle : 0.592 5.614 9954 Z= 0.308 Chirality : 0.045 0.159 1056 Planarity : 0.005 0.105 1310 Dihedral : 5.457 55.484 1000 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.88 % Allowed : 21.32 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.11 (0.29), residues: 882 helix: 0.80 (0.28), residues: 334 sheet: -0.88 (0.45), residues: 154 loop : -0.36 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.015 0.002 TYR A 13 PHE 0.016 0.002 PHE C 20 TRP 0.008 0.001 TRP A 63 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 ( 7368) covalent geometry : angle 0.59197 / 0.31 ( 9954) hydrogen bonds : bond 0.03673 / 2.36 ( 305) hydrogen bonds : angle 5.19820 / 3.73 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7493 (m-30) cc_final: 0.7267 (m-30) REVERT: A 207 GLN cc_start: 0.8645 (mm110) cc_final: 0.7754 (mm110) REVERT: A 210 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7765 (mtm-85) REVERT: A 246 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7841 (mmm160) REVERT: A 300 ARG cc_start: 0.8058 (ptp-170) cc_final: 0.7829 (ptp-170) REVERT: B 35 MET cc_start: 0.7609 (mtp) cc_final: 0.7384 (mtp) REVERT: C 203 TYR cc_start: 0.8245 (t80) cc_final: 0.7838 (t80) REVERT: C 241 ASN cc_start: 0.8136 (p0) cc_final: 0.7915 (p0) REVERT: C 278 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7250 (mm-30) outliers start: 30 outliers final: 19 residues processed: 231 average time/residue: 0.4599 time to fit residues: 111.4750 Evaluate side-chains 232 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 48 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN C 96 GLN C 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.134077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124694 restraints weight = 8935.987| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.30 r_work: 0.3592 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7368 Z= 0.156 Angle : 0.566 6.180 9954 Z= 0.292 Chirality : 0.044 0.156 1056 Planarity : 0.005 0.106 1310 Dihedral : 5.167 51.281 998 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.62 % Allowed : 22.87 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.01 (0.29), residues: 882 helix: 0.93 (0.29), residues: 334 sheet: -1.07 (0.43), residues: 166 loop : -0.20 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.009 0.001 TYR C 13 PHE 0.012 0.002 PHE C 20 TRP 0.010 0.001 TRP A 63 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7368) covalent geometry : angle 0.56602 / 0.29 ( 9954) hydrogen bonds : bond 0.03305 / 2.13 ( 305) hydrogen bonds : angle 5.05130 / 3.61 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8137 (mptt) cc_final: 0.7894 (mttp) REVERT: A 61 ASP cc_start: 0.7504 (m-30) cc_final: 0.7253 (m-30) REVERT: A 207 GLN cc_start: 0.8663 (mm110) cc_final: 0.7948 (mm110) REVERT: A 210 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7832 (mtm-85) REVERT: A 246 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7827 (mmm160) REVERT: B 35 MET cc_start: 0.7590 (mtp) cc_final: 0.7329 (mtp) REVERT: C 49 MET cc_start: 0.8430 (mtt) cc_final: 0.7768 (mtt) REVERT: C 161 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7847 (t80) REVERT: C 203 TYR cc_start: 0.8204 (t80) cc_final: 0.7822 (t80) REVERT: C 278 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7248 (mm-30) outliers start: 28 outliers final: 18 residues processed: 231 average time/residue: 0.4852 time to fit residues: 117.6566 Evaluate side-chains 230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.0030 chunk 74 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 145 HIS A 199 HIS A 241 ASN A 303 GLN C 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.134954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125494 restraints weight = 9058.336| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.32 r_work: 0.3603 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7368 Z= 0.144 Angle : 0.560 6.487 9954 Z= 0.291 Chirality : 0.044 0.171 1056 Planarity : 0.005 0.095 1310 Dihedral : 5.051 47.365 998 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.75 % Allowed : 23.51 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.14 (0.30), residues: 882 helix: 1.09 (0.29), residues: 334 sheet: -1.03 (0.43), residues: 166 loop : -0.12 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.017 0.001 TYR A 13 PHE 0.018 0.001 PHE A 59 TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7368) covalent geometry : angle 0.55987 / 0.29 ( 9954) hydrogen bonds : bond 0.03174 / 2.04 ( 305) hydrogen bonds : angle 4.94633 / 3.53 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8140 (mptt) cc_final: 0.7899 (mttp) REVERT: A 61 ASP cc_start: 0.7555 (m-30) cc_final: 0.7289 (m-30) REVERT: A 187 MET cc_start: 0.7893 (mtm) cc_final: 0.7692 (mtt) REVERT: A 246 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7802 (mmm160) REVERT: A 303 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6623 (tt0) REVERT: B 35 MET cc_start: 0.7672 (mtp) cc_final: 0.7436 (mtp) REVERT: C 48 MET cc_start: 0.8574 (mtt) cc_final: 0.8282 (mtt) REVERT: C 161 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7843 (t80) REVERT: C 203 TYR cc_start: 0.8198 (t80) cc_final: 0.7885 (t80) REVERT: C 278 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7223 (mm-30) outliers start: 29 outliers final: 17 residues processed: 231 average time/residue: 0.5000 time to fit residues: 120.8931 Evaluate side-chains 232 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 145 HIS A 241 ASN A 303 GLN C 96 GLN C 241 ASN C 313 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124487 restraints weight = 9083.430| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.31 r_work: 0.3586 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7368 Z= 0.195 Angle : 0.611 8.490 9954 Z= 0.314 Chirality : 0.046 0.226 1056 Planarity : 0.005 0.087 1310 Dihedral : 5.187 47.558 998 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.75 % Allowed : 24.03 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.05 (0.29), residues: 882 helix: 1.02 (0.29), residues: 334 sheet: -1.04 (0.43), residues: 168 loop : -0.20 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.016 0.002 TYR D 108 PHE 0.016 0.002 PHE C 20 TRP 0.011 0.001 TRP A 63 HIS 0.005 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 ( 7368) covalent geometry : angle 0.61114 / 0.31 ( 9954) hydrogen bonds : bond 0.03419 / 2.19 ( 305) hydrogen bonds : angle 4.98490 / 3.57 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8184 (mptt) cc_final: 0.7933 (mttp) REVERT: A 61 ASP cc_start: 0.7513 (m-30) cc_final: 0.7247 (m-30) REVERT: A 210 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7792 (mtm-85) REVERT: A 246 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7833 (mmm160) REVERT: B 35 MET cc_start: 0.7597 (mtp) cc_final: 0.7371 (mtp) REVERT: C 48 MET cc_start: 0.8580 (mtt) cc_final: 0.8301 (mtt) REVERT: C 161 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7853 (t80) REVERT: C 203 TYR cc_start: 0.8220 (t80) cc_final: 0.7924 (t80) REVERT: C 278 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: C 319 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7383 (mtm110) outliers start: 29 outliers final: 18 residues processed: 227 average time/residue: 0.4998 time to fit residues: 118.9798 Evaluate side-chains 230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.0040 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 30 optimal weight: 0.0020 overall best weight: 0.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 145 HIS A 244 ASN C 96 GLN C 145 HIS C 313 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128106 restraints weight = 9062.040| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.32 r_work: 0.3645 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7368 Z= 0.107 Angle : 0.560 8.052 9954 Z= 0.289 Chirality : 0.043 0.169 1056 Planarity : 0.005 0.087 1310 Dihedral : 4.825 42.680 998 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.10 % Allowed : 25.45 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.30 (0.30), residues: 882 helix: 1.19 (0.29), residues: 334 sheet: -0.96 (0.47), residues: 146 loop : -0.06 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.020 0.001 TYR A 13 PHE 0.014 0.001 PHE A 59 TRP 0.014 0.001 TRP A 63 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7368) covalent geometry : angle 0.56005 / 0.29 ( 9954) hydrogen bonds : bond 0.02786 / 1.80 ( 305) hydrogen bonds : angle 4.79783 / 3.41 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8058 (mptt) cc_final: 0.7824 (mttp) REVERT: A 52 PHE cc_start: 0.7567 (t80) cc_final: 0.7227 (t80) REVERT: A 61 ASP cc_start: 0.7530 (m-30) cc_final: 0.7294 (m-30) REVERT: A 193 ARG cc_start: 0.8214 (ptp90) cc_final: 0.7973 (ptp90) REVERT: A 232 ARG cc_start: 0.8355 (ttm170) cc_final: 0.8064 (ttp80) REVERT: A 246 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7797 (mmm160) REVERT: B 29 ARG cc_start: 0.8510 (ptt90) cc_final: 0.8203 (ptt-90) REVERT: C 48 MET cc_start: 0.8514 (mtt) cc_final: 0.8255 (mtt) REVERT: C 203 TYR cc_start: 0.8200 (t80) cc_final: 0.7952 (t80) REVERT: C 265 MET cc_start: 0.8923 (mmt) cc_final: 0.8525 (mmt) REVERT: C 319 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7298 (mtm110) outliers start: 24 outliers final: 14 residues processed: 233 average time/residue: 0.5050 time to fit residues: 123.3091 Evaluate side-chains 221 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 145 HIS A 158 HIS A 303 GLN C 96 GLN C 241 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.133616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124160 restraints weight = 8947.719| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.30 r_work: 0.3586 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7368 Z= 0.223 Angle : 0.642 7.722 9954 Z= 0.331 Chirality : 0.046 0.158 1056 Planarity : 0.005 0.079 1310 Dihedral : 5.172 43.918 998 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.97 % Allowed : 26.74 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.06 (0.29), residues: 882 helix: 1.01 (0.29), residues: 334 sheet: -0.97 (0.43), residues: 168 loop : -0.20 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 102 TYR 0.019 0.002 TYR D 108 PHE 0.018 0.002 PHE C 20 TRP 0.012 0.002 TRP A 63 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 7368) covalent geometry : angle 0.64194 / 0.33 ( 9954) hydrogen bonds : bond 0.03483 / 2.22 ( 305) hydrogen bonds : angle 4.94061 / 3.53 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8197 (mptt) cc_final: 0.7942 (mttp) REVERT: A 61 ASP cc_start: 0.7574 (m-30) cc_final: 0.7312 (m-30) REVERT: A 210 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7774 (mtm-85) REVERT: A 246 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7822 (mmm160) REVERT: C 48 MET cc_start: 0.8550 (mtt) cc_final: 0.8280 (mtt) REVERT: C 203 TYR cc_start: 0.8253 (t80) cc_final: 0.7982 (t80) REVERT: C 232 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8208 (mtm110) outliers start: 23 outliers final: 14 residues processed: 230 average time/residue: 0.4782 time to fit residues: 115.4612 Evaluate side-chains 230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 0.0670 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 145 HIS A 244 ASN C 96 GLN C 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126547 restraints weight = 9105.010| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.31 r_work: 0.3622 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7368 Z= 0.136 Angle : 0.593 7.899 9954 Z= 0.306 Chirality : 0.044 0.169 1056 Planarity : 0.005 0.086 1310 Dihedral : 4.972 43.479 998 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.33 % Allowed : 27.26 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.24 (0.30), residues: 882 helix: 1.20 (0.29), residues: 334 sheet: -0.94 (0.43), residues: 168 loop : -0.12 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.022 0.002 TYR A 13 PHE 0.014 0.001 PHE A 80 TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7368) covalent geometry : angle 0.59312 / 0.31 ( 9954) hydrogen bonds : bond 0.03013 / 1.92 ( 305) hydrogen bonds : angle 4.87271 / 3.46 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8130 (mptt) cc_final: 0.7888 (mttp) REVERT: A 42 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: A 61 ASP cc_start: 0.7561 (m-30) cc_final: 0.7322 (m-30) REVERT: A 210 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: A 246 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7776 (mmm160) REVERT: B 29 ARG cc_start: 0.8571 (ptt90) cc_final: 0.8280 (ptt-90) REVERT: C 48 MET cc_start: 0.8569 (mtt) cc_final: 0.8321 (mtt) REVERT: C 203 TYR cc_start: 0.8211 (t80) cc_final: 0.7923 (t80) REVERT: C 232 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8209 (mtm110) REVERT: C 319 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.7307 (mtm-85) outliers start: 18 outliers final: 15 residues processed: 225 average time/residue: 0.4762 time to fit residues: 112.3791 Evaluate side-chains 229 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 145 HIS C 96 GLN C 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124060 restraints weight = 9031.803| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.31 r_work: 0.3588 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7368 Z= 0.214 Angle : 0.642 7.735 9954 Z= 0.333 Chirality : 0.046 0.168 1056 Planarity : 0.005 0.079 1310 Dihedral : 5.200 43.885 998 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.10 % Allowed : 26.61 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.14 (0.30), residues: 882 helix: 1.13 (0.29), residues: 334 sheet: -0.98 (0.43), residues: 168 loop : -0.20 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.029 0.002 TYR D 27 PHE 0.017 0.002 PHE C 20 TRP 0.014 0.002 TRP A 63 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 7368) covalent geometry : angle 0.64249 / 0.33 ( 9954) hydrogen bonds : bond 0.03466 / 2.20 ( 305) hydrogen bonds : angle 4.96644 / 3.54 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.16 seconds wall clock time: 44 minutes 0.75 seconds (2640.75 seconds total)