Starting phenix.real_space_refine on Sat May 2 18:17:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua1_63975/05_2026/9ua1_63975_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua1_63975/05_2026/9ua1_63975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ua1_63975/05_2026/9ua1_63975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua1_63975/05_2026/9ua1_63975.map" model { file = "/net/cci-nas-00/data/ceres_data/9ua1_63975/05_2026/9ua1_63975_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua1_63975/05_2026/9ua1_63975_neut.cif" } resolution = 3.15 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= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5180 2.51 5 N 1331 2.21 5 O 1400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7947 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1938 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1954 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 14, 'TRANS': 235} Chain: "C" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1978 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 14, 'TRANS': 239} Chain: "D" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2013 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 15, 'TRANS': 240} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.24 Number of scatterers: 7947 At special positions: 0 Unit cell: (107, 82.39, 115.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1400 8.00 N 1331 7.00 C 5180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 469.8 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1862 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 63.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.718A pdb=" N PHE A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 81 through 114 removed outlier: 3.522A pdb=" N THR A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 Proline residue: A 123 - end of helix removed outlier: 3.504A pdb=" N PHE A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 144 removed outlier: 4.224A pdb=" N ILE A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 173 removed outlier: 4.110A pdb=" N ALA A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 219 Proline residue: A 203 - end of helix removed outlier: 3.773A pdb=" N GLY A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.659A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 245 through 275 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 81 through 114 removed outlier: 3.629A pdb=" N ARG B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 135 through 144 removed outlier: 4.201A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 173 removed outlier: 5.053A pdb=" N TRP B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 196 through 219 Proline residue: B 203 - end of helix removed outlier: 3.986A pdb=" N GLY B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 245 through 275 removed outlier: 3.599A pdb=" N TYR B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.545A pdb=" N ILE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.770A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.557A pdb=" N ASP C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 140 through 155 removed outlier: 4.043A pdb=" N VAL C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 188 removed outlier: 3.511A pdb=" N GLU C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.602A pdb=" N VAL C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 removed outlier: 4.409A pdb=" N TYR C 244 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.917A pdb=" N ALA D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 142 removed outlier: 3.853A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.790A pdb=" N ALA D 148 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.936A pdb=" N ILE D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 261 through 273 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.304A pdb=" N ILE C 28 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 9 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 8 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL C 65 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.332A pdb=" N MET C 81 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP C 163 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 83 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 208 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 209 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 223 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET C 211 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 37 through 48 removed outlier: 6.068A pdb=" N TYR D 38 " --> pdb=" O PRO D 32 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 40 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE D 30 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS D 42 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER D 28 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL D 44 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL D 27 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 79 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 96 through 99 removed outlier: 6.105A pdb=" N LEU D 176 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE D 211 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 224 " --> pdb=" O PHE D 53 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1374 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: 1.26 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2519 1.34 - 1.46: 1353 1.46 - 1.57: 4192 1.57 - 1.69: 10 1.69 - 1.81: 51 Bond restraints: 8125 Sorted by residual: bond pdb=" N ALA A 266 " pdb=" CA ALA A 266 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.19e-02 7.06e+03 3.04e+00 bond pdb=" N ALA B 266 " pdb=" CA ALA B 266 " ideal model delta sigma weight residual 1.459 1.479 -0.019 1.19e-02 7.06e+03 2.67e+00 bond pdb=" C ARG A 265 " pdb=" N ALA A 266 " ideal model delta sigma weight residual 1.334 1.350 -0.015 1.27e-02 6.20e+03 1.45e+00 bond pdb=" C ARG B 265 " pdb=" N ALA B 266 " ideal model delta sigma weight residual 1.334 1.350 -0.015 1.27e-02 6.20e+03 1.43e+00 bond pdb=" CA GLN D 180 " pdb=" C GLN D 180 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.82e-01 ... (remaining 8120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10895 1.62 - 3.24: 141 3.24 - 4.86: 25 4.86 - 6.48: 12 6.48 - 8.10: 3 Bond angle restraints: 11076 Sorted by residual: angle pdb=" C GLY D 102 " pdb=" N TYR D 103 " pdb=" CA TYR D 103 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.91e+00 angle pdb=" C GLN A 146 " pdb=" N ASN A 147 " pdb=" CA ASN A 147 " ideal model delta sigma weight residual 121.54 126.03 -4.49 1.91e+00 2.74e-01 5.52e+00 angle pdb=" CA LEU A 110 " pdb=" CB LEU A 110 " pdb=" CG LEU A 110 " ideal model delta sigma weight residual 116.30 124.39 -8.09 3.50e+00 8.16e-02 5.34e+00 angle pdb=" C ASN D 123 " pdb=" CA ASN D 123 " pdb=" CB ASN D 123 " ideal model delta sigma weight residual 110.34 112.94 -2.60 1.30e+00 5.92e-01 4.01e+00 angle pdb=" C GLN B 146 " pdb=" N ASN B 147 " pdb=" CA ASN B 147 " ideal model delta sigma weight residual 121.54 125.35 -3.81 1.91e+00 2.74e-01 3.98e+00 ... (remaining 11071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4197 17.88 - 35.76: 495 35.76 - 53.65: 139 53.65 - 71.53: 25 71.53 - 89.41: 17 Dihedral angle restraints: 4873 sinusoidal: 1980 harmonic: 2893 Sorted by residual: dihedral pdb=" CA ASN C 86 " pdb=" C ASN C 86 " pdb=" N TYR C 87 " pdb=" CA TYR C 87 " ideal model delta harmonic sigma weight residual 180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLY A 234 " pdb=" C GLY A 234 " pdb=" N PHE A 235 " pdb=" CA PHE A 235 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG A 265 " pdb=" C ARG A 265 " pdb=" N ALA A 266 " pdb=" CA ALA A 266 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 758 0.028 - 0.055: 332 0.055 - 0.083: 121 0.083 - 0.110: 65 0.110 - 0.138: 23 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA TRP A 161 " pdb=" N TRP A 161 " pdb=" C TRP A 161 " pdb=" CB TRP A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE C 228 " pdb=" N ILE C 228 " pdb=" C ILE C 228 " pdb=" CB ILE C 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1296 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 265 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ARG A 265 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG A 265 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A 266 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 265 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ARG B 265 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG B 265 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 266 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 73 " 0.013 2.00e-02 2.50e+03 1.80e-02 5.70e+00 pdb=" CG PHE A 73 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 73 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 73 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 73 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 73 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 73 " 0.000 2.00e-02 2.50e+03 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 63 2.62 - 3.19: 6867 3.19 - 3.76: 12827 3.76 - 4.33: 17808 4.33 - 4.90: 29568 Nonbonded interactions: 67133 Sorted by model distance: nonbonded pdb=" OG SER C 49 " pdb="MG MG C 702 " model vdw 2.044 2.170 nonbonded pdb=" O3B ATP C 701 " pdb="MG MG C 702 " model vdw 2.055 2.170 nonbonded pdb=" OE1 GLN C 85 " pdb="MG MG C 702 " model vdw 2.105 2.170 nonbonded pdb=" O ILE B 58 " pdb=" OG1 THR B 64 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG C 146 " pdb=" OG SER D 60 " model vdw 2.264 3.120 ... (remaining 67128 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' and resid 28 through 275) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.910 Find NCS groups from input model: 0.090 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8125 Z= 0.121 Angle : 0.527 8.097 11076 Z= 0.261 Chirality : 0.041 0.138 1299 Planarity : 0.004 0.049 1379 Dihedral : 17.460 89.410 3011 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.47 % Allowed : 20.52 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.27), residues: 1000 helix: 0.55 (0.21), residues: 603 sheet: 0.04 (0.63), residues: 68 loop : -1.37 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.009 0.001 TYR C 87 PHE 0.041 0.001 PHE A 73 TRP 0.012 0.001 TRP D 201 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8125) covalent geometry : angle 0.52743 (11076) hydrogen bonds : bond 0.23405 ( 467) hydrogen bonds : angle 6.68439 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.292 Fit side-chains REVERT: C 244 TYR cc_start: 0.7640 (m-10) cc_final: 0.7204 (m-10) REVERT: D 210 MET cc_start: 0.8849 (ttm) cc_final: 0.8616 (ttp) outliers start: 4 outliers final: 3 residues processed: 142 average time/residue: 0.1099 time to fit residues: 20.2987 Evaluate side-chains 140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.102616 restraints weight = 9380.558| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.65 r_work: 0.2954 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8125 Z= 0.157 Angle : 0.598 7.862 11076 Z= 0.305 Chirality : 0.044 0.177 1299 Planarity : 0.005 0.042 1379 Dihedral : 8.689 89.793 1157 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.95 % Allowed : 18.51 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.27), residues: 1000 helix: 0.98 (0.21), residues: 611 sheet: -0.24 (0.61), residues: 67 loop : -1.29 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 92 TYR 0.015 0.001 TYR C 122 PHE 0.013 0.001 PHE C 253 TRP 0.012 0.001 TRP D 201 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8125) covalent geometry : angle 0.59839 (11076) hydrogen bonds : bond 0.05718 ( 467) hydrogen bonds : angle 4.82793 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.305 Fit side-chains REVERT: B 186 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6960 (mm-40) REVERT: C 31 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: C 151 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7866 (ptt90) REVERT: D 146 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: D 175 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7137 (t) REVERT: D 210 MET cc_start: 0.8811 (ttm) cc_final: 0.8532 (ttp) REVERT: D 264 ASN cc_start: 0.7851 (m-40) cc_final: 0.7593 (m110) outliers start: 25 outliers final: 13 residues processed: 165 average time/residue: 0.1087 time to fit residues: 23.2746 Evaluate side-chains 156 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 191 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.102246 restraints weight = 9261.546| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.63 r_work: 0.2924 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8125 Z= 0.143 Angle : 0.563 7.964 11076 Z= 0.285 Chirality : 0.043 0.163 1299 Planarity : 0.004 0.046 1379 Dihedral : 8.212 83.507 1151 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.18 % Allowed : 19.69 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.27), residues: 1000 helix: 1.09 (0.21), residues: 611 sheet: -0.34 (0.61), residues: 67 loop : -1.32 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.017 0.001 TYR C 122 PHE 0.012 0.001 PHE C 253 TRP 0.013 0.001 TRP D 201 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8125) covalent geometry : angle 0.56339 (11076) hydrogen bonds : bond 0.05324 ( 467) hydrogen bonds : angle 4.61326 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.274 Fit side-chains REVERT: A 51 LYS cc_start: 0.6376 (mptt) cc_final: 0.5912 (mmmt) REVERT: B 71 PRO cc_start: 0.6724 (Cg_endo) cc_final: 0.6251 (Cg_exo) REVERT: B 227 MET cc_start: 0.6770 (ptp) cc_final: 0.6376 (ptt) REVERT: C 31 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: C 151 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7960 (ptt90) REVERT: D 146 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: D 210 MET cc_start: 0.8821 (ttm) cc_final: 0.8544 (ttp) REVERT: D 219 LEU cc_start: 0.8562 (mp) cc_final: 0.7982 (mp) outliers start: 27 outliers final: 16 residues processed: 155 average time/residue: 0.1118 time to fit residues: 22.2375 Evaluate side-chains 154 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101626 restraints weight = 9513.164| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.65 r_work: 0.2920 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8125 Z= 0.146 Angle : 0.565 8.373 11076 Z= 0.286 Chirality : 0.043 0.159 1299 Planarity : 0.004 0.048 1379 Dihedral : 7.992 79.530 1151 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.77 % Allowed : 20.05 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.27), residues: 1000 helix: 1.12 (0.21), residues: 611 sheet: -0.36 (0.62), residues: 65 loop : -1.30 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 96 TYR 0.018 0.001 TYR D 112 PHE 0.018 0.001 PHE C 253 TRP 0.015 0.001 TRP D 201 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8125) covalent geometry : angle 0.56501 (11076) hydrogen bonds : bond 0.05025 ( 467) hydrogen bonds : angle 4.48913 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.298 Fit side-chains REVERT: A 51 LYS cc_start: 0.6357 (mptt) cc_final: 0.5899 (mmmt) REVERT: B 71 PRO cc_start: 0.6752 (Cg_endo) cc_final: 0.6275 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8166 (mmt90) cc_final: 0.7682 (mmm-85) REVERT: B 227 MET cc_start: 0.6894 (ptp) cc_final: 0.6567 (ptt) REVERT: B 264 ASP cc_start: 0.8246 (t0) cc_final: 0.7892 (t0) REVERT: C 31 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: C 72 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7168 (tpp80) REVERT: C 180 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8098 (mmtp) REVERT: D 22 LEU cc_start: 0.8667 (tt) cc_final: 0.8199 (tp) REVERT: D 146 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: D 175 VAL cc_start: 0.7496 (OUTLIER) cc_final: 0.7166 (t) REVERT: D 219 LEU cc_start: 0.8569 (mp) cc_final: 0.8020 (mp) REVERT: D 264 ASN cc_start: 0.7981 (m-40) cc_final: 0.7556 (m-40) outliers start: 32 outliers final: 16 residues processed: 166 average time/residue: 0.1125 time to fit residues: 24.0882 Evaluate side-chains 162 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102660 restraints weight = 9368.757| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.64 r_work: 0.2959 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8125 Z= 0.135 Angle : 0.550 8.064 11076 Z= 0.278 Chirality : 0.043 0.167 1299 Planarity : 0.004 0.048 1379 Dihedral : 7.813 77.629 1151 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.13 % Allowed : 20.05 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.27), residues: 1000 helix: 1.13 (0.21), residues: 616 sheet: -0.33 (0.61), residues: 66 loop : -1.27 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.017 0.001 TYR D 112 PHE 0.015 0.001 PHE C 253 TRP 0.014 0.001 TRP D 201 HIS 0.002 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8125) covalent geometry : angle 0.54993 (11076) hydrogen bonds : bond 0.04819 ( 467) hydrogen bonds : angle 4.39923 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.269 Fit side-chains REVERT: A 51 LYS cc_start: 0.6276 (mptt) cc_final: 0.5805 (mmmt) REVERT: A 57 ASP cc_start: 0.7247 (m-30) cc_final: 0.6349 (t70) REVERT: B 71 PRO cc_start: 0.6809 (Cg_endo) cc_final: 0.6316 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7550 (mmm-85) REVERT: B 227 MET cc_start: 0.6932 (ptp) cc_final: 0.6632 (ptt) REVERT: B 264 ASP cc_start: 0.8291 (t0) cc_final: 0.7930 (t0) REVERT: B 272 ASN cc_start: 0.6851 (m-40) cc_final: 0.6582 (t0) REVERT: C 31 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: C 72 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.7079 (tpp80) REVERT: C 151 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7947 (ptt90) REVERT: C 180 LYS cc_start: 0.8295 (mmtp) cc_final: 0.8067 (mmtp) REVERT: D 23 ARG cc_start: 0.7549 (tmt-80) cc_final: 0.7161 (ttm-80) REVERT: D 146 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: D 175 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7167 (t) REVERT: D 210 MET cc_start: 0.8845 (ttm) cc_final: 0.8565 (ttp) REVERT: D 219 LEU cc_start: 0.8550 (mp) cc_final: 0.8004 (mp) REVERT: D 264 ASN cc_start: 0.7921 (m-40) cc_final: 0.7646 (m-40) outliers start: 35 outliers final: 19 residues processed: 169 average time/residue: 0.1146 time to fit residues: 24.6833 Evaluate side-chains 163 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN C 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103424 restraints weight = 9302.378| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.63 r_work: 0.3007 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8125 Z= 0.124 Angle : 0.539 7.760 11076 Z= 0.271 Chirality : 0.042 0.165 1299 Planarity : 0.004 0.047 1379 Dihedral : 7.643 75.448 1151 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.01 % Allowed : 19.81 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.27), residues: 1000 helix: 1.19 (0.21), residues: 616 sheet: -0.29 (0.61), residues: 66 loop : -1.24 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.019 0.001 TYR D 112 PHE 0.014 0.001 PHE C 253 TRP 0.014 0.001 TRP D 201 HIS 0.008 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8125) covalent geometry : angle 0.53866 (11076) hydrogen bonds : bond 0.04638 ( 467) hydrogen bonds : angle 4.31943 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.277 Fit side-chains REVERT: A 51 LYS cc_start: 0.6253 (mptt) cc_final: 0.5787 (mmmt) REVERT: A 57 ASP cc_start: 0.7083 (m-30) cc_final: 0.6304 (t70) REVERT: B 71 PRO cc_start: 0.6816 (Cg_endo) cc_final: 0.6319 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8106 (mmt90) cc_final: 0.7484 (mmm-85) REVERT: B 227 MET cc_start: 0.7000 (ptp) cc_final: 0.6703 (ptt) REVERT: B 264 ASP cc_start: 0.8305 (t0) cc_final: 0.7900 (t0) REVERT: B 272 ASN cc_start: 0.6866 (m-40) cc_final: 0.6654 (t0) REVERT: C 31 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6887 (mt0) REVERT: C 117 ASP cc_start: 0.6802 (m-30) cc_final: 0.6525 (m-30) REVERT: C 151 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7982 (ptt90) REVERT: C 180 LYS cc_start: 0.8277 (mmtp) cc_final: 0.8048 (mmtp) REVERT: D 23 ARG cc_start: 0.7560 (tmt-80) cc_final: 0.7154 (ttm-80) REVERT: D 146 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: D 175 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7140 (t) REVERT: D 210 MET cc_start: 0.8856 (ttm) cc_final: 0.8585 (ttp) REVERT: D 219 LEU cc_start: 0.8549 (mp) cc_final: 0.8009 (mp) REVERT: D 264 ASN cc_start: 0.7922 (m-40) cc_final: 0.7618 (m-40) outliers start: 34 outliers final: 19 residues processed: 173 average time/residue: 0.1149 time to fit residues: 25.3713 Evaluate side-chains 166 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103763 restraints weight = 9395.389| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.64 r_work: 0.3023 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8125 Z= 0.121 Angle : 0.538 7.591 11076 Z= 0.271 Chirality : 0.042 0.165 1299 Planarity : 0.004 0.046 1379 Dihedral : 7.561 75.828 1151 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.54 % Allowed : 20.05 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.27), residues: 1000 helix: 1.24 (0.21), residues: 616 sheet: 0.05 (0.66), residues: 55 loop : -1.22 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 96 TYR 0.019 0.001 TYR D 112 PHE 0.014 0.001 PHE C 253 TRP 0.014 0.001 TRP D 201 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8125) covalent geometry : angle 0.53805 (11076) hydrogen bonds : bond 0.04538 ( 467) hydrogen bonds : angle 4.28954 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.287 Fit side-chains REVERT: A 51 LYS cc_start: 0.6391 (mptt) cc_final: 0.5960 (mmmt) REVERT: A 57 ASP cc_start: 0.7031 (m-30) cc_final: 0.6358 (t70) REVERT: B 71 PRO cc_start: 0.6794 (Cg_endo) cc_final: 0.6292 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7828 (mmm-85) REVERT: B 227 MET cc_start: 0.6976 (ptp) cc_final: 0.6686 (ptt) REVERT: B 272 ASN cc_start: 0.6864 (m-40) cc_final: 0.6641 (t0) REVERT: C 31 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6894 (mt0) REVERT: C 117 ASP cc_start: 0.6523 (m-30) cc_final: 0.6220 (m-30) REVERT: C 151 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7955 (ptt90) REVERT: C 180 LYS cc_start: 0.8268 (mmtp) cc_final: 0.8045 (mmtp) REVERT: D 23 ARG cc_start: 0.7568 (tmt-80) cc_final: 0.7156 (ttm-80) REVERT: D 146 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7220 (pt0) REVERT: D 175 VAL cc_start: 0.7474 (OUTLIER) cc_final: 0.7155 (t) REVERT: D 210 MET cc_start: 0.8877 (ttm) cc_final: 0.8599 (ttp) REVERT: D 219 LEU cc_start: 0.8551 (mp) cc_final: 0.8019 (mp) outliers start: 30 outliers final: 18 residues processed: 172 average time/residue: 0.1152 time to fit residues: 25.3578 Evaluate side-chains 168 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103456 restraints weight = 9394.089| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.60 r_work: 0.2973 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8125 Z= 0.144 Angle : 0.569 8.605 11076 Z= 0.285 Chirality : 0.043 0.174 1299 Planarity : 0.004 0.047 1379 Dihedral : 7.610 75.250 1151 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.77 % Allowed : 20.28 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.27), residues: 1000 helix: 1.15 (0.21), residues: 616 sheet: -0.05 (0.67), residues: 54 loop : -1.26 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.020 0.001 TYR D 112 PHE 0.021 0.001 PHE C 253 TRP 0.016 0.001 TRP D 201 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8125) covalent geometry : angle 0.56930 (11076) hydrogen bonds : bond 0.04765 ( 467) hydrogen bonds : angle 4.31646 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.295 Fit side-chains REVERT: A 51 LYS cc_start: 0.6301 (mptt) cc_final: 0.5859 (mmmt) REVERT: A 57 ASP cc_start: 0.7082 (m-30) cc_final: 0.6403 (t70) REVERT: A 59 MET cc_start: 0.7087 (ttp) cc_final: 0.6631 (tpt) REVERT: B 71 PRO cc_start: 0.6736 (Cg_endo) cc_final: 0.6216 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8132 (mmt90) cc_final: 0.7790 (mmm-85) REVERT: B 272 ASN cc_start: 0.6889 (m-40) cc_final: 0.6623 (t0) REVERT: B 274 ILE cc_start: 0.8009 (mt) cc_final: 0.7691 (mm) REVERT: C 31 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: C 117 ASP cc_start: 0.6539 (m-30) cc_final: 0.6248 (m-30) REVERT: C 151 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7946 (ptt90) REVERT: C 180 LYS cc_start: 0.8297 (mmtp) cc_final: 0.8069 (mmtp) REVERT: D 23 ARG cc_start: 0.7590 (tmt-80) cc_final: 0.7174 (ttm-80) REVERT: D 146 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: D 175 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7142 (t) REVERT: D 219 LEU cc_start: 0.8564 (mp) cc_final: 0.8034 (mp) outliers start: 32 outliers final: 23 residues processed: 171 average time/residue: 0.1145 time to fit residues: 24.9062 Evaluate side-chains 171 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103240 restraints weight = 9343.435| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.65 r_work: 0.2924 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8125 Z= 0.128 Angle : 0.553 7.889 11076 Z= 0.277 Chirality : 0.043 0.175 1299 Planarity : 0.004 0.047 1379 Dihedral : 7.563 76.242 1151 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.42 % Allowed : 19.93 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.27), residues: 1000 helix: 1.20 (0.21), residues: 616 sheet: -0.03 (0.67), residues: 54 loop : -1.25 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 96 TYR 0.021 0.001 TYR D 112 PHE 0.042 0.001 PHE A 73 TRP 0.014 0.001 TRP D 201 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8125) covalent geometry : angle 0.55316 (11076) hydrogen bonds : bond 0.04597 ( 467) hydrogen bonds : angle 4.27149 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.274 Fit side-chains REVERT: A 51 LYS cc_start: 0.6286 (mptt) cc_final: 0.5832 (mmmt) REVERT: A 57 ASP cc_start: 0.7045 (m-30) cc_final: 0.6367 (t70) REVERT: A 59 MET cc_start: 0.7114 (ttp) cc_final: 0.6632 (tpt) REVERT: B 71 PRO cc_start: 0.6813 (Cg_endo) cc_final: 0.6299 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7790 (mmm-85) REVERT: B 272 ASN cc_start: 0.6849 (m-40) cc_final: 0.6601 (t0) REVERT: C 31 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6935 (mt0) REVERT: C 104 ASP cc_start: 0.7691 (m-30) cc_final: 0.7387 (m-30) REVERT: C 117 ASP cc_start: 0.6532 (m-30) cc_final: 0.6242 (m-30) REVERT: C 151 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7984 (ptt90) REVERT: C 180 LYS cc_start: 0.8259 (mmtp) cc_final: 0.8040 (mmtp) REVERT: D 23 ARG cc_start: 0.7600 (tmt-80) cc_final: 0.7152 (ttm-80) REVERT: D 146 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: D 175 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.7173 (t) REVERT: D 219 LEU cc_start: 0.8545 (mp) cc_final: 0.8004 (mp) outliers start: 29 outliers final: 24 residues processed: 168 average time/residue: 0.1150 time to fit residues: 24.4774 Evaluate side-chains 172 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103111 restraints weight = 9286.458| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.64 r_work: 0.2924 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8125 Z= 0.133 Angle : 0.560 8.212 11076 Z= 0.281 Chirality : 0.043 0.176 1299 Planarity : 0.004 0.047 1379 Dihedral : 7.561 76.614 1151 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.66 % Allowed : 19.81 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.27), residues: 1000 helix: 1.19 (0.21), residues: 616 sheet: -0.05 (0.66), residues: 54 loop : -1.26 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 96 TYR 0.022 0.001 TYR D 112 PHE 0.035 0.001 PHE A 73 TRP 0.017 0.001 TRP D 201 HIS 0.009 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8125) covalent geometry : angle 0.56028 (11076) hydrogen bonds : bond 0.04645 ( 467) hydrogen bonds : angle 4.27026 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.287 Fit side-chains REVERT: A 51 LYS cc_start: 0.6244 (mptt) cc_final: 0.5775 (mmmt) REVERT: A 57 ASP cc_start: 0.7059 (m-30) cc_final: 0.6387 (t70) REVERT: A 59 MET cc_start: 0.7130 (ttp) cc_final: 0.6654 (tpt) REVERT: B 43 LEU cc_start: 0.6446 (mt) cc_final: 0.6197 (mt) REVERT: B 71 PRO cc_start: 0.6829 (Cg_endo) cc_final: 0.6308 (Cg_exo) REVERT: B 210 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7829 (mmm-85) REVERT: B 272 ASN cc_start: 0.6825 (m-40) cc_final: 0.6580 (t0) REVERT: C 31 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6988 (mt0) REVERT: C 104 ASP cc_start: 0.7746 (m-30) cc_final: 0.7415 (m-30) REVERT: C 117 ASP cc_start: 0.6635 (m-30) cc_final: 0.6339 (m-30) REVERT: C 151 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7938 (ptt90) REVERT: C 180 LYS cc_start: 0.8277 (mmtp) cc_final: 0.8053 (mmtp) REVERT: D 22 LEU cc_start: 0.8624 (tt) cc_final: 0.8339 (tp) REVERT: D 23 ARG cc_start: 0.7580 (tmt-80) cc_final: 0.7156 (ttm-80) REVERT: D 146 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: D 175 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7202 (t) REVERT: D 219 LEU cc_start: 0.8545 (mp) cc_final: 0.8012 (mp) outliers start: 31 outliers final: 23 residues processed: 166 average time/residue: 0.1143 time to fit residues: 24.0794 Evaluate side-chains 169 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 0.0070 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105564 restraints weight = 9211.927| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.63 r_work: 0.2962 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8125 Z= 0.112 Angle : 0.537 7.507 11076 Z= 0.269 Chirality : 0.042 0.170 1299 Planarity : 0.004 0.046 1379 Dihedral : 7.487 80.526 1151 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.83 % Allowed : 20.52 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.27), residues: 1000 helix: 1.35 (0.21), residues: 610 sheet: 0.11 (0.64), residues: 60 loop : -1.24 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 96 TYR 0.022 0.001 TYR D 112 PHE 0.033 0.001 PHE A 73 TRP 0.013 0.001 TRP D 201 HIS 0.008 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8125) covalent geometry : angle 0.53679 (11076) hydrogen bonds : bond 0.04357 ( 467) hydrogen bonds : angle 4.20916 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.05 seconds wall clock time: 37 minutes 5.71 seconds (2225.71 seconds total)