Starting phenix.real_space_refine on Thu Jun 4 22:33:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7d_70195/06_2026/9o7d_70195.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7d_70195/06_2026/9o7d_70195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7d_70195/06_2026/9o7d_70195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7d_70195/06_2026/9o7d_70195.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7d_70195/06_2026/9o7d_70195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7d_70195/06_2026/9o7d_70195.map" } resolution = 3.6 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= -0.000 sd= 0.031 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 S 41 5.16 5 C 4867 2.51 5 N 1373 2.21 5 O 1537 1.98 5 H 7603 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15421 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4487 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "B" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4487 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "C" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3301 Classifications: {'peptide': 224} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "D" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3146 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Time building chain proxies: 3.18, per 1000 atoms: 0.21 Number of scatterers: 15421 At special positions: 0 Unit cell: (98.412, 112.59, 150.954, 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 41 16.00 O 1537 8.00 N 1373 7.00 C 4867 6.00 H 7603 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.02 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 211 " distance=2.02 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 104 " distance=2.06 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 213 " distance=2.04 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: 1.29 Conformation dependent library (CDL) restraints added in 452.1 milliseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 13 sheets defined 46.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 26 through 39 Processing helix chain 'A' and resid 41 through 56 Processing helix chain 'A' and resid 59 through 73 removed outlier: 4.161A pdb=" N TYR A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.947A pdb=" N GLU A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.530A pdb=" N SER A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 189 through 217 removed outlier: 3.815A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 41 through 56 Processing helix chain 'B' and resid 59 through 72 removed outlier: 4.329A pdb=" N TYR B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 109 through 127 Processing helix chain 'B' and resid 134 through 184 removed outlier: 3.840A pdb=" N HIS B 184 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 224 removed outlier: 3.663A pdb=" N LYS B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 66 through 69 removed outlier: 3.725A pdb=" N GLN C 69 " --> pdb=" O GLN C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 201 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 251 through 253 Processing sheet with id=AA2, first strand: chain 'B' and resid 251 through 253 Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AA4, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.317A pdb=" N GLY C 37 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 38 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP C 54 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 40 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.171A pdb=" N TYR C 191 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.171A pdb=" N TYR C 191 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.697A pdb=" N VAL D 25 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 100 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP D 51 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.697A pdb=" N VAL D 25 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 100 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 38 Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.546A pdb=" N VAL D 153 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR D 151 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU D 200 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 153 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU D 198 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU D 155 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER D 196 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER D 157 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 194 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.546A pdb=" N VAL D 153 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR D 151 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU D 200 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 153 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU D 198 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU D 155 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER D 196 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER D 157 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 194 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.475A pdb=" N TRP D 168 " --> pdb=" O VAL D 175 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1257 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: 3.17 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 7586 1.13 - 1.30: 1362 1.30 - 1.47: 3034 1.47 - 1.65: 3542 1.65 - 1.82: 57 Bond restraints: 15581 Sorted by residual: bond pdb=" CD1 PHE C 99 " pdb=" HD1 PHE C 99 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" CD2 PHE B 98 " pdb=" HD2 PHE B 98 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CD2 PHE C 181 " pdb=" HD2 PHE C 181 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CH2 TRP C 118 " pdb=" HH2 TRP C 118 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" CD1 PHE C 137 " pdb=" HD1 PHE C 137 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.50e+01 ... (remaining 15576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 24644 2.61 - 5.22: 2480 5.22 - 7.83: 912 7.83 - 10.44: 24 10.44 - 13.05: 17 Bond angle restraints: 28077 Sorted by residual: angle pdb=" N PHE B 237 " pdb=" CA PHE B 237 " pdb=" C PHE B 237 " ideal model delta sigma weight residual 112.24 118.36 -6.12 1.28e+00 6.10e-01 2.29e+01 angle pdb=" C TYR C 36 " pdb=" N GLY C 37 " pdb=" CA GLY C 37 " ideal model delta sigma weight residual 120.60 125.13 -4.53 1.01e+00 9.80e-01 2.02e+01 angle pdb=" C GLU B 242 " pdb=" N PRO B 243 " pdb=" CA PRO B 243 " ideal model delta sigma weight residual 119.76 124.28 -4.52 1.03e+00 9.43e-01 1.92e+01 angle pdb=" C MET B 73 " pdb=" CA MET B 73 " pdb=" CB MET B 73 " ideal model delta sigma weight residual 116.54 110.23 6.31 1.46e+00 4.69e-01 1.87e+01 angle pdb=" C PHE B 131 " pdb=" N GLY B 132 " pdb=" CA GLY B 132 " ideal model delta sigma weight residual 119.92 124.03 -4.11 9.60e-01 1.09e+00 1.84e+01 ... (remaining 28072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 7000 16.88 - 33.75: 239 33.75 - 50.63: 98 50.63 - 67.51: 50 67.51 - 84.38: 5 Dihedral angle restraints: 7392 sinusoidal: 4033 harmonic: 3359 Sorted by residual: dihedral pdb=" CA PRO D 133 " pdb=" C PRO D 133 " pdb=" N SER D 134 " pdb=" CA SER D 134 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA THR D 112 " pdb=" C THR D 112 " pdb=" N ALA D 113 " pdb=" CA ALA D 113 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE C 99 " pdb=" C PHE C 99 " pdb=" N CYS C 100 " pdb=" CA CYS C 100 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 825 0.056 - 0.111: 212 0.111 - 0.166: 101 0.166 - 0.222: 25 0.222 - 0.277: 5 Chirality restraints: 1168 Sorted by residual: chirality pdb=" CA ASP D 158 " pdb=" N ASP D 158 " pdb=" C ASP D 158 " pdb=" CB ASP D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ASN D 190 " pdb=" N ASN D 190 " pdb=" C ASN D 190 " pdb=" CB ASN D 190 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ASN D 43 " pdb=" N ASN D 43 " pdb=" C ASN D 43 " pdb=" CB ASN D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1165 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " -0.152 2.00e-02 2.50e+03 5.94e-02 1.06e+02 pdb=" CG PHE C 115 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE C 115 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE C 115 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE C 115 " -0.043 2.00e-02 2.50e+03 pdb=" HE2 PHE C 115 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE C 115 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 187 " 0.066 2.00e-02 2.50e+03 6.26e-02 5.88e+01 pdb=" CD GLN D 187 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN D 187 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 GLN D 187 " -0.062 2.00e-02 2.50e+03 pdb="HE21 GLN D 187 " 0.106 2.00e-02 2.50e+03 pdb="HE22 GLN D 187 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 63 " -0.092 2.00e-02 2.50e+03 3.81e-02 4.34e+01 pdb=" CG TYR B 63 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 63 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 63 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 63 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 63 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 63 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 63 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR B 63 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR B 63 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 63 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR B 63 " 0.008 2.00e-02 2.50e+03 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 1692 2.27 - 2.85: 31797 2.85 - 3.43: 41973 3.43 - 4.02: 55397 4.02 - 4.60: 80452 Nonbonded interactions: 211311 Sorted by model distance: nonbonded pdb=" HG SER D 212 " pdb=" OE2 GLU D 223 " model vdw 1.681 2.450 nonbonded pdb=" HG SER C 143 " pdb=" OXT SER D 232 " model vdw 1.690 2.450 nonbonded pdb=" OE2 GLU D 144 " pdb=" HG1 THR D 151 " model vdw 1.692 2.450 nonbonded pdb=" O ALA B 79 " pdb=" HG CYS B 83 " model vdw 1.695 2.620 nonbonded pdb=" O ILE B 235 " pdb=" HG SER B 236 " model vdw 1.703 2.450 ... (remaining 211306 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 : 0.013 0.062 7982 Z= 0.808 Angle : 1.382 7.883 10806 Z= 0.958 Chirality : 0.066 0.277 1168 Planarity : 0.008 0.071 1422 Dihedral : 10.964 84.382 2987 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.14 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.12 (0.25), residues: 988 helix: 1.17 (0.23), residues: 409 sheet: 1.33 (0.38), residues: 166 loop : 0.19 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 66 TYR 0.078 0.006 TYR B 63 PHE 0.084 0.006 PHE C 115 TRP 0.021 0.003 TRP D 107 HIS 0.012 0.001 HIS D 208 Details of bonding type rmsd/Z covalent geometry : bond 0.01282 / 0.81 ( 7978) covalent geometry : angle 1.38085 / 0.96 (10798) SS BOND : bond 0.01414 / 0.50 ( 4) SS BOND : angle 2.62119 / 1.52 ( 8) hydrogen bonds : bond 0.19440 / 13.03 ( 445) hydrogen bonds : angle 6.39036 / 4.53 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7997 (m-30) cc_final: 0.7737 (m-30) REVERT: A 245 ILE cc_start: 0.7979 (mt) cc_final: 0.7761 (mt) REVERT: A 271 THR cc_start: 0.7260 (p) cc_final: 0.6447 (p) REVERT: B 40 ARG cc_start: 0.8027 (mpt180) cc_final: 0.7556 (ttt90) REVERT: B 183 ASN cc_start: 0.8355 (m-40) cc_final: 0.7857 (t0) REVERT: B 214 LEU cc_start: 0.8918 (tp) cc_final: 0.8711 (tt) REVERT: C 117 ILE cc_start: 0.8928 (mt) cc_final: 0.8608 (tp) REVERT: C 122 THR cc_start: 0.6731 (m) cc_final: 0.6505 (m) REVERT: C 158 LYS cc_start: 0.7865 (ptmm) cc_final: 0.7470 (pttm) REVERT: C 225 LYS cc_start: 0.8187 (tttt) cc_final: 0.7837 (ttmm) REVERT: D 158 ASP cc_start: 0.8541 (m-30) cc_final: 0.8336 (p0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3053 time to fit residues: 99.3751 Evaluate side-chains 162 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN C 110 ASN D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.158558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.117569 restraints weight = 52144.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.120383 restraints weight = 19256.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.121312 restraints weight = 11477.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121953 restraints weight = 11170.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.122407 restraints weight = 9392.065| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7982 Z= 0.160 Angle : 0.650 12.847 10806 Z= 0.355 Chirality : 0.041 0.155 1168 Planarity : 0.005 0.054 1422 Dihedral : 4.629 32.960 1097 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.24 % Favored : 96.36 % Rotamer: Outliers : 1.41 % Allowed : 9.18 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.58 (0.26), residues: 988 helix: 2.07 (0.24), residues: 418 sheet: 1.12 (0.34), residues: 198 loop : -0.13 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 84 TYR 0.011 0.001 TYR A 164 PHE 0.020 0.002 PHE A 98 TRP 0.005 0.001 TRP C 40 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 7978) covalent geometry : angle 0.64372 / 0.35 (10798) SS BOND : bond 0.00721 / 0.33 ( 4) SS BOND : angle 3.49393 / 1.50 ( 8) hydrogen bonds : bond 0.05862 / 3.94 ( 445) hydrogen bonds : angle 4.97847 / 3.54 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8933 (mttt) cc_final: 0.8630 (tptt) REVERT: A 210 ASP cc_start: 0.8419 (m-30) cc_final: 0.8122 (m-30) REVERT: B 40 ARG cc_start: 0.8216 (mpt180) cc_final: 0.7633 (ttt90) REVERT: B 70 TYR cc_start: 0.7957 (m-80) cc_final: 0.7452 (m-80) REVERT: B 121 TYR cc_start: 0.8151 (t80) cc_final: 0.7804 (t80) REVERT: B 183 ASN cc_start: 0.8743 (m-40) cc_final: 0.8227 (t0) REVERT: B 256 ASP cc_start: 0.7629 (m-30) cc_final: 0.7384 (m-30) REVERT: C 117 ILE cc_start: 0.8959 (mt) cc_final: 0.8644 (tp) outliers start: 12 outliers final: 9 residues processed: 171 average time/residue: 0.3029 time to fit residues: 63.7883 Evaluate side-chains 131 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 44 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 92 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 162 HIS C 61 ASN C 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.155907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.111026 restraints weight = 52564.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.115806 restraints weight = 19752.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.119243 restraints weight = 11315.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.120831 restraints weight = 8210.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.121933 restraints weight = 7017.326| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7982 Z= 0.144 Angle : 0.590 8.317 10806 Z= 0.319 Chirality : 0.039 0.144 1168 Planarity : 0.004 0.050 1422 Dihedral : 4.420 30.203 1097 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.15 % Favored : 95.65 % Rotamer: Outliers : 1.65 % Allowed : 10.94 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.70 (0.27), residues: 988 helix: 2.35 (0.25), residues: 417 sheet: 0.95 (0.34), residues: 197 loop : -0.15 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 140 TYR 0.021 0.001 TYR C 191 PHE 0.025 0.001 PHE A 293 TRP 0.004 0.001 TRP C 169 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7978) covalent geometry : angle 0.58602 / 0.32 (10798) SS BOND : bond 0.00417 / 0.16 ( 4) SS BOND : angle 2.58978 / 1.08 ( 8) hydrogen bonds : bond 0.04821 / 3.25 ( 445) hydrogen bonds : angle 4.74939 / 3.36 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8928 (mttt) cc_final: 0.8673 (tptt) REVERT: A 210 ASP cc_start: 0.8243 (m-30) cc_final: 0.7995 (m-30) REVERT: B 40 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7656 (ttt90) REVERT: B 70 TYR cc_start: 0.7759 (m-80) cc_final: 0.7254 (m-80) REVERT: B 211 MET cc_start: 0.8938 (tmm) cc_final: 0.8107 (tmm) REVERT: C 117 ILE cc_start: 0.8990 (mt) cc_final: 0.8644 (tp) outliers start: 14 outliers final: 12 residues processed: 149 average time/residue: 0.2622 time to fit residues: 49.3518 Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.148845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.106943 restraints weight = 52845.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.105997 restraints weight = 22484.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107453 restraints weight = 16536.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107345 restraints weight = 12998.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.107848 restraints weight = 13434.731| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 7982 Z= 0.258 Angle : 0.659 6.140 10806 Z= 0.364 Chirality : 0.042 0.156 1168 Planarity : 0.005 0.057 1422 Dihedral : 4.845 42.092 1097 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 2.82 % Allowed : 10.82 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.14 (0.27), residues: 988 helix: 2.27 (0.25), residues: 408 sheet: 0.08 (0.33), residues: 202 loop : -0.52 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 241 TYR 0.021 0.002 TYR D 197 PHE 0.027 0.003 PHE C 33 TRP 0.045 0.003 TRP A 299 HIS 0.005 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.26 ( 7978) covalent geometry : angle 0.65753 / 0.36 (10798) SS BOND : bond 0.00641 / 0.21 ( 4) SS BOND : angle 1.84816 / 0.84 ( 8) hydrogen bonds : bond 0.04303 / 2.84 ( 445) hydrogen bonds : angle 4.89047 / 3.45 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9060 (mttt) cc_final: 0.8773 (tptt) REVERT: A 210 ASP cc_start: 0.8404 (m-30) cc_final: 0.8082 (m-30) REVERT: A 286 MET cc_start: 0.9208 (tpt) cc_final: 0.8838 (tpt) REVERT: B 40 ARG cc_start: 0.8253 (mpt180) cc_final: 0.7890 (ttt90) REVERT: B 70 TYR cc_start: 0.7911 (m-80) cc_final: 0.7362 (m-80) REVERT: B 211 MET cc_start: 0.8833 (tmm) cc_final: 0.8152 (tmm) REVERT: B 286 MET cc_start: 0.8421 (mmm) cc_final: 0.7970 (mmm) REVERT: D 209 LYS cc_start: 0.8938 (tttt) cc_final: 0.8731 (ttpp) outliers start: 24 outliers final: 21 residues processed: 130 average time/residue: 0.2797 time to fit residues: 45.8198 Evaluate side-chains 117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.150431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.110311 restraints weight = 52552.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.108950 restraints weight = 25172.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.109194 restraints weight = 17247.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.110222 restraints weight = 15139.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109955 restraints weight = 13524.925| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7982 Z= 0.136 Angle : 0.561 5.272 10806 Z= 0.303 Chirality : 0.039 0.136 1168 Planarity : 0.004 0.048 1422 Dihedral : 4.561 39.610 1097 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 12.12 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.45 (0.27), residues: 988 helix: 2.57 (0.25), residues: 413 sheet: 0.25 (0.33), residues: 196 loop : -0.46 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.014 0.001 TYR D 102 PHE 0.012 0.001 PHE A 98 TRP 0.014 0.001 TRP A 299 HIS 0.008 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7978) covalent geometry : angle 0.55948 / 0.30 (10798) SS BOND : bond 0.00434 / 0.15 ( 4) SS BOND : angle 1.57436 / 0.64 ( 8) hydrogen bonds : bond 0.03851 / 2.55 ( 445) hydrogen bonds : angle 4.52287 / 3.18 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9040 (mttt) cc_final: 0.8745 (tptt) REVERT: A 210 ASP cc_start: 0.8359 (m-30) cc_final: 0.8039 (m-30) REVERT: B 40 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7849 (ttt90) REVERT: B 70 TYR cc_start: 0.7896 (m-80) cc_final: 0.7290 (m-80) REVERT: B 211 MET cc_start: 0.8752 (tmm) cc_final: 0.8001 (tmm) REVERT: D 44 ILE cc_start: 0.8053 (mm) cc_final: 0.7668 (mm) REVERT: D 209 LYS cc_start: 0.8982 (tttt) cc_final: 0.8681 (ttpp) outliers start: 16 outliers final: 13 residues processed: 123 average time/residue: 0.2641 time to fit residues: 41.1279 Evaluate side-chains 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.149123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.101400 restraints weight = 52485.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.106055 restraints weight = 20407.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.108914 restraints weight = 12141.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110511 restraints weight = 9225.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.111062 restraints weight = 8035.457| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7982 Z= 0.156 Angle : 0.561 6.697 10806 Z= 0.302 Chirality : 0.039 0.151 1168 Planarity : 0.005 0.082 1422 Dihedral : 4.547 41.349 1097 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 2.12 % Allowed : 12.12 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.44 (0.27), residues: 988 helix: 2.63 (0.25), residues: 415 sheet: 0.11 (0.33), residues: 200 loop : -0.48 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 84 TYR 0.012 0.002 TYR D 102 PHE 0.024 0.002 PHE A 98 TRP 0.005 0.001 TRP C 169 HIS 0.004 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 7978) covalent geometry : angle 0.55821 / 0.30 (10798) SS BOND : bond 0.00485 / 0.17 ( 4) SS BOND : angle 2.10271 / 0.83 ( 8) hydrogen bonds : bond 0.03656 / 2.44 ( 445) hydrogen bonds : angle 4.43499 / 3.13 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9056 (mttt) cc_final: 0.8780 (tptt) REVERT: A 210 ASP cc_start: 0.8175 (m-30) cc_final: 0.7899 (m-30) REVERT: B 40 ARG cc_start: 0.8242 (mpt180) cc_final: 0.7836 (ttt90) REVERT: B 70 TYR cc_start: 0.7795 (m-80) cc_final: 0.7168 (m-80) REVERT: B 211 MET cc_start: 0.8806 (tmm) cc_final: 0.8033 (tmm) REVERT: C 87 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4997 (tp) REVERT: D 44 ILE cc_start: 0.8048 (mm) cc_final: 0.7701 (mm) REVERT: D 209 LYS cc_start: 0.8879 (tttt) cc_final: 0.8675 (ttpp) outliers start: 18 outliers final: 17 residues processed: 117 average time/residue: 0.2690 time to fit residues: 39.6685 Evaluate side-chains 117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.145422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099459 restraints weight = 52669.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.101316 restraints weight = 22074.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101931 restraints weight = 15102.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102872 restraints weight = 13489.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.102859 restraints weight = 11765.563| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 7982 Z= 0.329 Angle : 0.700 6.832 10806 Z= 0.389 Chirality : 0.044 0.177 1168 Planarity : 0.006 0.081 1422 Dihedral : 5.336 65.012 1097 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.38 % Favored : 93.42 % Rotamer: Outliers : 3.65 % Allowed : 12.00 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 988 helix: 2.14 (0.24), residues: 415 sheet: -0.68 (0.33), residues: 205 loop : -1.32 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 241 TYR 0.029 0.003 TYR D 52 PHE 0.021 0.003 PHE C 33 TRP 0.037 0.003 TRP A 299 HIS 0.006 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.33 ( 7978) covalent geometry : angle 0.69819 / 0.39 (10798) SS BOND : bond 0.00633 / 0.20 ( 4) SS BOND : angle 2.07051 / 0.87 ( 8) hydrogen bonds : bond 0.04080 / 2.66 ( 445) hydrogen bonds : angle 4.90028 / 3.46 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9106 (mttt) cc_final: 0.8840 (tptt) REVERT: A 210 ASP cc_start: 0.8328 (m-30) cc_final: 0.8043 (m-30) REVERT: A 286 MET cc_start: 0.9278 (tpt) cc_final: 0.8869 (tpt) REVERT: B 40 ARG cc_start: 0.8345 (mpt180) cc_final: 0.7859 (ttt90) REVERT: B 70 TYR cc_start: 0.7938 (m-80) cc_final: 0.7713 (m-80) REVERT: B 211 MET cc_start: 0.8783 (tmm) cc_final: 0.8150 (tmm) REVERT: C 8 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8538 (mp) REVERT: D 209 LYS cc_start: 0.9026 (tttt) cc_final: 0.8693 (ttpp) outliers start: 31 outliers final: 22 residues processed: 128 average time/residue: 0.2413 time to fit residues: 39.9142 Evaluate side-chains 117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 182 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.147826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.099161 restraints weight = 52742.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.103609 restraints weight = 20393.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.106511 restraints weight = 12237.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.107834 restraints weight = 9390.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.107833 restraints weight = 8231.039| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7982 Z= 0.128 Angle : 0.570 5.932 10806 Z= 0.306 Chirality : 0.040 0.149 1168 Planarity : 0.005 0.088 1422 Dihedral : 4.960 61.990 1097 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.76 % Favored : 95.04 % Rotamer: Outliers : 1.88 % Allowed : 14.00 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.13 (0.27), residues: 988 helix: 2.72 (0.25), residues: 415 sheet: -0.38 (0.34), residues: 200 loop : -0.90 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 84 TYR 0.018 0.001 TYR C 209 PHE 0.025 0.002 PHE A 98 TRP 0.026 0.001 TRP A 299 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7978) covalent geometry : angle 0.56758 / 0.31 (10798) SS BOND : bond 0.00322 / 0.10 ( 4) SS BOND : angle 1.83724 / 0.72 ( 8) hydrogen bonds : bond 0.03483 / 2.29 ( 445) hydrogen bonds : angle 4.38246 / 3.11 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9092 (mttt) cc_final: 0.8807 (tptt) REVERT: A 210 ASP cc_start: 0.8272 (m-30) cc_final: 0.7977 (m-30) REVERT: B 40 ARG cc_start: 0.8264 (mpt180) cc_final: 0.7812 (ttt90) REVERT: B 70 TYR cc_start: 0.7777 (m-80) cc_final: 0.7489 (m-80) REVERT: B 211 MET cc_start: 0.8819 (tmm) cc_final: 0.8091 (tmm) REVERT: D 44 ILE cc_start: 0.8032 (mm) cc_final: 0.7710 (mm) REVERT: D 209 LYS cc_start: 0.8946 (tttt) cc_final: 0.8674 (ttpp) outliers start: 16 outliers final: 15 residues processed: 110 average time/residue: 0.2575 time to fit residues: 36.1376 Evaluate side-chains 107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.146809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.097965 restraints weight = 52675.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.102421 restraints weight = 20708.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104990 restraints weight = 12557.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106736 restraints weight = 9690.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106783 restraints weight = 8351.786| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7982 Z= 0.177 Angle : 0.576 5.679 10806 Z= 0.314 Chirality : 0.040 0.151 1168 Planarity : 0.005 0.062 1422 Dihedral : 4.954 65.195 1097 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 1.88 % Allowed : 14.12 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.05 (0.27), residues: 988 helix: 2.72 (0.25), residues: 414 sheet: -0.43 (0.33), residues: 205 loop : -1.01 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.022 0.002 TYR B 164 PHE 0.020 0.002 PHE A 98 TRP 0.020 0.001 TRP A 299 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 7978) covalent geometry : angle 0.57387 / 0.31 (10798) SS BOND : bond 0.00384 / 0.12 ( 4) SS BOND : angle 1.70781 / 0.67 ( 8) hydrogen bonds : bond 0.03471 / 2.28 ( 445) hydrogen bonds : angle 4.41946 / 3.13 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9106 (mttt) cc_final: 0.8828 (tptt) REVERT: A 210 ASP cc_start: 0.8262 (m-30) cc_final: 0.7965 (m-30) REVERT: B 40 ARG cc_start: 0.8275 (mpt180) cc_final: 0.7833 (ttt90) REVERT: B 70 TYR cc_start: 0.7730 (m-80) cc_final: 0.7470 (m-80) REVERT: B 211 MET cc_start: 0.8783 (tmm) cc_final: 0.8066 (tmm) REVERT: D 44 ILE cc_start: 0.8038 (mm) cc_final: 0.7718 (mm) REVERT: D 209 LYS cc_start: 0.8905 (tttt) cc_final: 0.8653 (ttpp) outliers start: 16 outliers final: 15 residues processed: 106 average time/residue: 0.2730 time to fit residues: 36.7058 Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.147863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.099358 restraints weight = 53092.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.103950 restraints weight = 20471.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.106455 restraints weight = 12241.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.108336 restraints weight = 9391.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.108954 restraints weight = 8104.499| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7982 Z= 0.125 Angle : 0.544 5.478 10806 Z= 0.293 Chirality : 0.039 0.142 1168 Planarity : 0.004 0.055 1422 Dihedral : 4.794 63.923 1097 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 1.76 % Allowed : 14.47 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.34 (0.28), residues: 988 helix: 2.97 (0.25), residues: 408 sheet: -0.31 (0.34), residues: 200 loop : -0.79 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.015 0.001 TYR C 209 PHE 0.031 0.001 PHE A 98 TRP 0.020 0.001 TRP A 299 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7978) covalent geometry : angle 0.54258 / 0.29 (10798) SS BOND : bond 0.00298 / 0.09 ( 4) SS BOND : angle 1.65862 / 0.64 ( 8) hydrogen bonds : bond 0.03226 / 2.13 ( 445) hydrogen bonds : angle 4.21200 / 2.99 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9105 (mttt) cc_final: 0.8843 (tptt) REVERT: A 210 ASP cc_start: 0.8225 (m-30) cc_final: 0.7935 (m-30) REVERT: B 40 ARG cc_start: 0.8271 (mpt180) cc_final: 0.7828 (ttt90) REVERT: B 70 TYR cc_start: 0.7699 (m-80) cc_final: 0.7420 (m-80) REVERT: B 211 MET cc_start: 0.8772 (tmm) cc_final: 0.8052 (tmm) REVERT: D 44 ILE cc_start: 0.7905 (mm) cc_final: 0.7596 (mm) REVERT: D 209 LYS cc_start: 0.8896 (tttt) cc_final: 0.8645 (ttpp) outliers start: 15 outliers final: 14 residues processed: 105 average time/residue: 0.2504 time to fit residues: 33.7496 Evaluate side-chains 107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.146824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099338 restraints weight = 52934.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.103953 restraints weight = 21656.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104283 restraints weight = 12884.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104167 restraints weight = 12679.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.104698 restraints weight = 12484.090| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7982 Z= 0.177 Angle : 0.561 5.476 10806 Z= 0.307 Chirality : 0.040 0.141 1168 Planarity : 0.005 0.062 1422 Dihedral : 4.933 69.441 1097 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.38 % Favored : 93.42 % Rotamer: Outliers : 2.35 % Allowed : 13.88 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.14 (0.28), residues: 988 helix: 2.88 (0.25), residues: 408 sheet: -0.46 (0.34), residues: 205 loop : -0.97 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 153 TYR 0.013 0.002 TYR D 52 PHE 0.025 0.002 PHE A 98 TRP 0.016 0.002 TRP A 299 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 7978) covalent geometry : angle 0.55965 / 0.31 (10798) SS BOND : bond 0.00351 / 0.11 ( 4) SS BOND : angle 1.57931 / 0.63 ( 8) hydrogen bonds : bond 0.03325 / 2.20 ( 445) hydrogen bonds : angle 4.30349 / 3.05 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3440.51 seconds wall clock time: 59 minutes 8.97 seconds (3548.97 seconds total)