Starting phenix.real_space_refine on Fri Feb 14 00:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q5h_18179/02_2025/8q5h_18179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q5h_18179/02_2025/8q5h_18179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q5h_18179/02_2025/8q5h_18179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q5h_18179/02_2025/8q5h_18179.map" model { file = "/net/cci-nas-00/data/ceres_data/8q5h_18179/02_2025/8q5h_18179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q5h_18179/02_2025/8q5h_18179.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6085 2.51 5 N 1625 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9574 Number of models: 1 Model: "" Number of chains: 7 Chain: "4" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 530 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "5" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 835 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1693 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1724 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "K" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1744 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200} Chain: "N" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1622 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Time building chain proxies: 5.57, per 1000 atoms: 0.58 Number of scatterers: 9574 At special positions: 0 Unit cell: (208.08, 187.68, 134.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1818 8.00 N 1625 7.00 C 6085 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 69.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain '4' and resid 131 through 148 Processing helix chain '4' and resid 181 through 193 removed outlier: 3.719A pdb=" N VAL 4 193 " --> pdb=" O LEU 4 189 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 141 Processing helix chain '5' and resid 194 through 204 Processing helix chain '5' and resid 207 through 221 Processing helix chain '5' and resid 222 through 224 No H-bonds generated for 'chain '5' and resid 222 through 224' Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 16 through 50 removed outlier: 3.653A pdb=" N CYS A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 87 removed outlier: 3.813A pdb=" N HIS A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 110 through 170 removed outlier: 3.792A pdb=" N HIS A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 205 removed outlier: 3.514A pdb=" N SER A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 52 removed outlier: 4.186A pdb=" N LEU B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 69 through 98 removed outlier: 3.627A pdb=" N TYR B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 116 removed outlier: 3.671A pdb=" N VAL B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 189 removed outlier: 3.933A pdb=" N VAL B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Proline residue: B 139 - end of helix removed outlier: 3.549A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 removed outlier: 4.307A pdb=" N GLU B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 150 Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 161 through 183 Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.574A pdb=" N CYS D 191 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE D 192 " --> pdb=" O GLN D 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 188 through 192' Processing helix chain 'D' and resid 203 through 245 removed outlier: 3.796A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 3.664A pdb=" N LEU D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 327 removed outlier: 3.524A pdb=" N ILE D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 removed outlier: 3.597A pdb=" N LYS D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 2192 through 2208 Processing helix chain 'K' and resid 2211 through 2216 Processing helix chain 'K' and resid 2221 through 2250 removed outlier: 3.506A pdb=" N VAL K2232 " --> pdb=" O GLU K2228 " (cutoff:3.500A) Processing helix chain 'K' and resid 2251 through 2253 No H-bonds generated for 'chain 'K' and resid 2251 through 2253' Processing helix chain 'K' and resid 2305 through 2316 removed outlier: 3.713A pdb=" N ILE K2309 " --> pdb=" O SER K2305 " (cutoff:3.500A) Processing helix chain 'K' and resid 2321 through 2335 Processing helix chain 'N' and resid 43 through 54 Processing helix chain 'N' and resid 54 through 62 Processing helix chain 'N' and resid 68 through 87 removed outlier: 3.687A pdb=" N ALA N 72 " --> pdb=" O ILE N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 151 removed outlier: 3.864A pdb=" N ILE N 108 " --> pdb=" O MET N 104 " (cutoff:3.500A) Proline residue: N 130 - end of helix removed outlier: 3.552A pdb=" N LYS N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 213 removed outlier: 3.533A pdb=" N LYS N 189 " --> pdb=" O SER N 185 " (cutoff:3.500A) Proline residue: N 192 - end of helix Proline residue: N 209 - end of helix Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 265 through 270 Processing sheet with id=AA1, first strand: chain '4' and resid 149 through 151 Processing sheet with id=AA2, first strand: chain '5' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS 5 153 " --> pdb=" O ILE 5 149 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS 5 175 " --> pdb=" O VAL 5 184 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL 5 184 " --> pdb=" O HIS 5 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 2135 through 2140 removed outlier: 6.585A pdb=" N VAL K2146 " --> pdb=" O VAL K2138 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP K2140 " --> pdb=" O GLN K2144 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN K2144 " --> pdb=" O TRP K2140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 2258 through 2259 removed outlier: 6.553A pdb=" N GLU K2279 " --> pdb=" O ASN K2299 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN K2299 " --> pdb=" O GLU K2279 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR K2281 " --> pdb=" O ILE K2297 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE K2297 " --> pdb=" O THR K2281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 38 through 39 removed outlier: 5.369A pdb=" N VAL N 38 " --> pdb=" O SER N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 658 hydrogen bonds defined for protein. 1956 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: 2.70 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2986 1.34 - 1.45: 1272 1.45 - 1.57: 5434 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9762 Sorted by residual: bond pdb=" C ALA N 167 " pdb=" N PRO N 168 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.94e+00 bond pdb=" CG ARG 5 130 " pdb=" CD ARG 5 130 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CA GLN B 67 " pdb=" CB GLN B 67 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.56e+00 bond pdb=" CG1 ILE K2243 " pdb=" CD1 ILE K2243 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.96e+00 bond pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 ... (remaining 9757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 12872 2.30 - 4.59: 255 4.59 - 6.89: 33 6.89 - 9.19: 7 9.19 - 11.48: 4 Bond angle restraints: 13171 Sorted by residual: angle pdb=" C LEU A 98 " pdb=" N LEU A 99 " pdb=" CA LEU A 99 " ideal model delta sigma weight residual 121.03 130.64 -9.61 1.60e+00 3.91e-01 3.61e+01 angle pdb=" N GLN B 67 " pdb=" CA GLN B 67 " pdb=" C GLN B 67 " ideal model delta sigma weight residual 107.23 114.58 -7.35 1.67e+00 3.59e-01 1.94e+01 angle pdb=" CG ARG 5 130 " pdb=" CD ARG 5 130 " pdb=" NE ARG 5 130 " ideal model delta sigma weight residual 112.00 103.52 8.48 2.20e+00 2.07e-01 1.49e+01 angle pdb=" CB MET A 71 " pdb=" CG MET A 71 " pdb=" SD MET A 71 " ideal model delta sigma weight residual 112.70 124.18 -11.48 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CB MET D 211 " pdb=" CG MET D 211 " pdb=" SD MET D 211 " ideal model delta sigma weight residual 112.70 101.26 11.44 3.00e+00 1.11e-01 1.45e+01 ... (remaining 13166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5382 17.93 - 35.86: 492 35.86 - 53.80: 75 53.80 - 71.73: 28 71.73 - 89.66: 24 Dihedral angle restraints: 6001 sinusoidal: 2527 harmonic: 3474 Sorted by residual: dihedral pdb=" CA MET 5 171 " pdb=" C MET 5 171 " pdb=" N PHE 5 172 " pdb=" CA PHE 5 172 " ideal model delta harmonic sigma weight residual 180.00 149.48 30.52 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA GLN B 67 " pdb=" C GLN B 67 " pdb=" N LEU B 68 " pdb=" CA LEU B 68 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LEU A 89 " pdb=" C LEU A 89 " pdb=" N ILE A 90 " pdb=" CA ILE A 90 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1125 0.047 - 0.095: 261 0.095 - 0.142: 61 0.142 - 0.190: 4 0.190 - 0.237: 1 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA TYR N 129 " pdb=" N TYR N 129 " pdb=" C TYR N 129 " pdb=" CB TYR N 129 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL K2180 " pdb=" N VAL K2180 " pdb=" C VAL K2180 " pdb=" CB VAL K2180 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA GLU D 150 " pdb=" N GLU D 150 " pdb=" C GLU D 150 " pdb=" CB GLU D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1449 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 130 " -0.251 9.50e-02 1.11e+02 1.13e-01 8.70e+00 pdb=" NE ARG 5 130 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG 5 130 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 130 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 130 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 115 " -0.018 2.00e-02 2.50e+03 1.99e-02 6.93e+00 pdb=" CG PHE N 115 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE N 115 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE N 115 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE N 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE N 115 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE N 115 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 4 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 5 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " -0.034 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 127 2.64 - 3.20: 9229 3.20 - 3.77: 15325 3.77 - 4.33: 19328 4.33 - 4.90: 30707 Nonbonded interactions: 74716 Sorted by model distance: nonbonded pdb=" O ARG 5 141 " pdb=" NH1 ARG 5 141 " model vdw 2.072 3.120 nonbonded pdb=" OH TYR B 62 " pdb=" O THR B 73 " model vdw 2.119 3.040 nonbonded pdb=" OE2 GLU B 156 " pdb=" OG SER D 263 " model vdw 2.146 3.040 nonbonded pdb=" O THR A 16 " pdb=" OG1 THR A 19 " model vdw 2.148 3.040 nonbonded pdb=" OG SER D 160 " pdb=" OE1 GLU D 162 " model vdw 2.152 3.040 ... (remaining 74711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.050 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4656 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 : 0.004 0.055 9762 Z= 0.229 Angle : 0.816 11.481 13171 Z= 0.474 Chirality : 0.043 0.237 1452 Planarity : 0.006 0.113 1709 Dihedral : 15.487 89.660 3727 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1155 helix: 1.24 (0.19), residues: 748 sheet: -1.52 (0.61), residues: 77 loop : -0.89 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K2212 HIS 0.011 0.001 HIS K2234 PHE 0.046 0.002 PHE N 115 TYR 0.021 0.001 TYR N 129 ARG 0.017 0.001 ARG 5 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.041 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: 4 159 MET cc_start: 0.5922 (ppp) cc_final: 0.4886 (ppp) REVERT: A 68 LEU cc_start: 0.8989 (tp) cc_final: 0.8630 (tt) REVERT: A 145 GLN cc_start: 0.8148 (mt0) cc_final: 0.7359 (mt0) REVERT: B 72 MET cc_start: 0.8923 (mtt) cc_final: 0.8570 (tpt) REVERT: D 220 LEU cc_start: 0.9402 (mt) cc_final: 0.9113 (mt) REVERT: K 2179 ASP cc_start: 0.8366 (t0) cc_final: 0.7724 (t0) REVERT: K 2181 ASN cc_start: 0.6364 (p0) cc_final: 0.5178 (p0) REVERT: K 2241 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7032 (pt0) REVERT: N 175 CYS cc_start: 0.8391 (m) cc_final: 0.8008 (p) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2999 time to fit residues: 101.1050 Evaluate side-chains 140 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 143 GLN B 144 GLN B 183 GLN B 194 GLN D 147 GLN D 231 HIS D 301 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.100968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.085534 restraints weight = 79879.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.087146 restraints weight = 53139.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.088297 restraints weight = 39212.924| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9762 Z= 0.198 Angle : 0.677 10.430 13171 Z= 0.347 Chirality : 0.043 0.158 1452 Planarity : 0.006 0.073 1709 Dihedral : 4.334 30.446 1258 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.37 % Allowed : 4.01 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1155 helix: 1.47 (0.18), residues: 744 sheet: -1.63 (0.60), residues: 77 loop : -0.82 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K2212 HIS 0.007 0.001 HIS B 134 PHE 0.039 0.002 PHE N 115 TYR 0.018 0.001 TYR 4 153 ARG 0.010 0.001 ARG 5 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 1.152 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: 4 159 MET cc_start: 0.5275 (ppp) cc_final: 0.4377 (ppp) REVERT: 5 171 MET cc_start: 0.5079 (mmp) cc_final: 0.4787 (mmp) REVERT: 5 197 PHE cc_start: 0.7738 (m-10) cc_final: 0.7407 (m-10) REVERT: 5 199 GLU cc_start: 0.8879 (tp30) cc_final: 0.8661 (tm-30) REVERT: A 61 ARG cc_start: 0.8669 (tpt170) cc_final: 0.8450 (tpt170) REVERT: A 145 GLN cc_start: 0.9054 (mt0) cc_final: 0.8118 (mt0) REVERT: A 187 LYS cc_start: 0.9282 (mppt) cc_final: 0.9068 (mmtt) REVERT: B 72 MET cc_start: 0.9355 (mtt) cc_final: 0.8727 (tpt) REVERT: D 270 THR cc_start: 0.8752 (t) cc_final: 0.8383 (p) REVERT: D 325 MET cc_start: 0.8093 (mmm) cc_final: 0.7769 (mmm) REVERT: K 2155 GLN cc_start: 0.8220 (tt0) cc_final: 0.7712 (tp-100) REVERT: K 2156 LEU cc_start: 0.8430 (tt) cc_final: 0.7944 (tt) REVERT: K 2179 ASP cc_start: 0.9084 (t0) cc_final: 0.8287 (t0) REVERT: K 2181 ASN cc_start: 0.7482 (p0) cc_final: 0.6474 (p0) REVERT: K 2241 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7133 (pt0) REVERT: K 2256 MET cc_start: 0.3494 (ptm) cc_final: 0.3020 (ptp) REVERT: N 175 CYS cc_start: 0.8529 (m) cc_final: 0.8104 (p) REVERT: N 269 TRP cc_start: 0.8283 (m100) cc_final: 0.7779 (m100) outliers start: 4 outliers final: 0 residues processed: 176 average time/residue: 0.3046 time to fit residues: 70.4244 Evaluate side-chains 123 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.0030 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 GLN A 164 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.099724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.084359 restraints weight = 81621.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.086137 restraints weight = 55080.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.087341 restraints weight = 40708.500| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9762 Z= 0.178 Angle : 0.649 11.717 13171 Z= 0.331 Chirality : 0.042 0.170 1452 Planarity : 0.005 0.050 1709 Dihedral : 4.360 31.826 1258 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1155 helix: 1.41 (0.18), residues: 748 sheet: -1.84 (0.59), residues: 75 loop : -0.87 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K2249 HIS 0.005 0.001 HIS N 217 PHE 0.030 0.002 PHE N 115 TYR 0.013 0.001 TYR K2245 ARG 0.015 0.001 ARG 5 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.108 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: 4 159 MET cc_start: 0.7187 (ppp) cc_final: 0.6321 (ppp) REVERT: 4 180 LEU cc_start: 0.7112 (tp) cc_final: 0.6490 (tt) REVERT: A 79 PHE cc_start: 0.8887 (m-80) cc_final: 0.8383 (m-80) REVERT: A 175 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7278 (mmm160) REVERT: B 41 MET cc_start: 0.0551 (ppp) cc_final: 0.0216 (ppp) REVERT: B 72 MET cc_start: 0.9390 (mtt) cc_final: 0.8697 (tpt) REVERT: D 126 VAL cc_start: 0.7066 (t) cc_final: 0.6840 (t) REVERT: K 2152 ASP cc_start: 0.7741 (m-30) cc_final: 0.7090 (t70) REVERT: K 2155 GLN cc_start: 0.8091 (tt0) cc_final: 0.7797 (tp-100) REVERT: K 2156 LEU cc_start: 0.8330 (tt) cc_final: 0.7812 (tt) REVERT: K 2179 ASP cc_start: 0.9128 (t0) cc_final: 0.8614 (t0) REVERT: K 2236 CYS cc_start: 0.8038 (m) cc_final: 0.6761 (t) REVERT: K 2241 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7199 (pt0) REVERT: N 175 CYS cc_start: 0.8550 (m) cc_final: 0.8138 (p) REVERT: N 269 TRP cc_start: 0.8099 (m100) cc_final: 0.7641 (m100) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.2720 time to fit residues: 59.6530 Evaluate side-chains 125 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.097536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.082672 restraints weight = 81824.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.084631 restraints weight = 55853.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.085376 restraints weight = 36910.475| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9762 Z= 0.179 Angle : 0.665 9.955 13171 Z= 0.339 Chirality : 0.043 0.187 1452 Planarity : 0.005 0.047 1709 Dihedral : 4.327 31.363 1258 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1155 helix: 1.39 (0.18), residues: 749 sheet: -1.86 (0.55), residues: 80 loop : -0.85 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K2249 HIS 0.004 0.001 HIS B 134 PHE 0.025 0.002 PHE N 115 TYR 0.012 0.001 TYR K2245 ARG 0.010 0.001 ARG 5 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.097 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: 4 159 MET cc_start: 0.7442 (ppp) cc_final: 0.6572 (ppp) REVERT: 4 180 LEU cc_start: 0.7469 (tp) cc_final: 0.6955 (tt) REVERT: A 79 PHE cc_start: 0.8847 (m-80) cc_final: 0.8591 (m-80) REVERT: A 93 ILE cc_start: 0.7808 (pt) cc_final: 0.7460 (mm) REVERT: A 175 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7662 (mmm160) REVERT: B 41 MET cc_start: -0.0429 (ppp) cc_final: -0.0778 (ppp) REVERT: B 72 MET cc_start: 0.9324 (mtt) cc_final: 0.8606 (tpt) REVERT: B 137 MET cc_start: 0.5932 (ppp) cc_final: 0.5678 (ppp) REVERT: D 231 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8805 (t70) REVERT: D 292 MET cc_start: 0.8087 (tmm) cc_final: 0.6948 (ppp) REVERT: K 2155 GLN cc_start: 0.8139 (tt0) cc_final: 0.7902 (tp40) REVERT: K 2156 LEU cc_start: 0.8508 (tt) cc_final: 0.7962 (tt) REVERT: K 2167 PHE cc_start: 0.6664 (p90) cc_final: 0.6417 (p90) REVERT: K 2175 ARG cc_start: 0.7206 (ttt180) cc_final: 0.6517 (mmm160) REVERT: K 2179 ASP cc_start: 0.9200 (t0) cc_final: 0.8754 (t0) REVERT: K 2239 LEU cc_start: 0.9020 (tp) cc_final: 0.8601 (tt) REVERT: N 175 CYS cc_start: 0.8703 (m) cc_final: 0.8223 (p) REVERT: N 269 TRP cc_start: 0.8292 (m100) cc_final: 0.7698 (m100) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2566 time to fit residues: 56.0747 Evaluate side-chains 120 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 7.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** 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 = 0.4409 r_free = 0.4409 target = 0.097113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.082222 restraints weight = 82363.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.083878 restraints weight = 58590.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.085575 restraints weight = 39164.371| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9762 Z= 0.168 Angle : 0.637 9.360 13171 Z= 0.327 Chirality : 0.042 0.147 1452 Planarity : 0.004 0.040 1709 Dihedral : 4.251 31.726 1258 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1155 helix: 1.43 (0.18), residues: 750 sheet: -1.80 (0.56), residues: 80 loop : -0.78 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K2249 HIS 0.004 0.001 HIS K2234 PHE 0.021 0.002 PHE A 28 TYR 0.010 0.001 TYR K2245 ARG 0.010 0.001 ARG 5 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.292 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: 4 159 MET cc_start: 0.7574 (ppp) cc_final: 0.6678 (ppp) REVERT: 4 180 LEU cc_start: 0.7486 (tp) cc_final: 0.6765 (tt) REVERT: A 79 PHE cc_start: 0.8725 (m-80) cc_final: 0.8441 (m-80) REVERT: A 175 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7826 (mmm160) REVERT: B 72 MET cc_start: 0.9303 (mtt) cc_final: 0.8652 (tpt) REVERT: B 137 MET cc_start: 0.6207 (ppp) cc_final: 0.5883 (ppp) REVERT: D 133 ARG cc_start: 0.8496 (mmm160) cc_final: 0.7541 (mtt90) REVERT: D 292 MET cc_start: 0.8100 (tmm) cc_final: 0.7324 (ppp) REVERT: K 2152 ASP cc_start: 0.7834 (m-30) cc_final: 0.7136 (t70) REVERT: K 2155 GLN cc_start: 0.8202 (tt0) cc_final: 0.7983 (tp40) REVERT: K 2156 LEU cc_start: 0.8691 (tt) cc_final: 0.7994 (tt) REVERT: K 2167 PHE cc_start: 0.6352 (p90) cc_final: 0.5991 (p90) REVERT: K 2175 ARG cc_start: 0.6927 (ttt180) cc_final: 0.6167 (mmm160) REVERT: K 2179 ASP cc_start: 0.9231 (t0) cc_final: 0.8556 (t0) REVERT: K 2181 ASN cc_start: 0.7743 (p0) cc_final: 0.6886 (p0) REVERT: K 2256 MET cc_start: 0.5077 (ptm) cc_final: 0.4584 (ptp) REVERT: N 175 CYS cc_start: 0.8746 (m) cc_final: 0.8284 (p) REVERT: N 207 MET cc_start: 0.7978 (mtt) cc_final: 0.7613 (mtp) REVERT: N 269 TRP cc_start: 0.8329 (m100) cc_final: 0.7844 (m100) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2801 time to fit residues: 56.7607 Evaluate side-chains 111 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.0030 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS D 314 GLN ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.096184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.080721 restraints weight = 83225.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.082485 restraints weight = 56283.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.083684 restraints weight = 41915.201| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9762 Z= 0.169 Angle : 0.644 9.729 13171 Z= 0.332 Chirality : 0.043 0.150 1452 Planarity : 0.004 0.040 1709 Dihedral : 4.218 30.932 1258 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 0.19 % Allowed : 2.24 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1155 helix: 1.45 (0.18), residues: 752 sheet: -1.50 (0.56), residues: 82 loop : -0.74 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K2249 HIS 0.007 0.001 HIS 4 174 PHE 0.027 0.002 PHE A 33 TYR 0.010 0.001 TYR K2174 ARG 0.007 0.001 ARG 5 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.150 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: 4 159 MET cc_start: 0.7771 (ppp) cc_final: 0.6799 (ppp) REVERT: 4 180 LEU cc_start: 0.7636 (tp) cc_final: 0.7294 (tp) REVERT: A 79 PHE cc_start: 0.8792 (m-80) cc_final: 0.8364 (m-80) REVERT: A 93 ILE cc_start: 0.7962 (mm) cc_final: 0.7637 (pt) REVERT: A 175 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7775 (mmm160) REVERT: B 41 MET cc_start: -0.0468 (ppp) cc_final: -0.0681 (ppp) REVERT: B 72 MET cc_start: 0.9277 (mtt) cc_final: 0.8588 (tpt) REVERT: B 137 MET cc_start: 0.6363 (ppp) cc_final: 0.5938 (ppp) REVERT: D 133 ARG cc_start: 0.8311 (mmm160) cc_final: 0.7428 (mtt180) REVERT: K 2152 ASP cc_start: 0.7784 (m-30) cc_final: 0.7159 (t70) REVERT: K 2155 GLN cc_start: 0.8094 (tt0) cc_final: 0.7675 (tt0) REVERT: K 2175 ARG cc_start: 0.6505 (ttt180) cc_final: 0.5934 (mmm160) REVERT: K 2179 ASP cc_start: 0.9247 (t0) cc_final: 0.8766 (t0) REVERT: K 2256 MET cc_start: 0.5665 (ptm) cc_final: 0.5067 (ptp) REVERT: N 175 CYS cc_start: 0.8706 (m) cc_final: 0.8262 (p) REVERT: N 269 TRP cc_start: 0.8412 (m100) cc_final: 0.7903 (m100) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.2521 time to fit residues: 51.0248 Evaluate side-chains 113 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 184 ASN B 153 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.094998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.079828 restraints weight = 83646.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.081773 restraints weight = 57253.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.082546 restraints weight = 38446.600| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9762 Z= 0.172 Angle : 0.651 10.570 13171 Z= 0.333 Chirality : 0.042 0.169 1452 Planarity : 0.004 0.046 1709 Dihedral : 4.214 30.604 1258 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1155 helix: 1.46 (0.18), residues: 752 sheet: -1.40 (0.57), residues: 82 loop : -0.74 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 78 HIS 0.005 0.001 HIS 4 174 PHE 0.025 0.002 PHE A 33 TYR 0.034 0.001 TYR A 31 ARG 0.011 0.001 ARG 5 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.087 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: 4 159 MET cc_start: 0.7824 (ppp) cc_final: 0.6830 (ppp) REVERT: 4 180 LEU cc_start: 0.7703 (tp) cc_final: 0.7385 (tp) REVERT: A 79 PHE cc_start: 0.8890 (m-80) cc_final: 0.8564 (m-80) REVERT: A 93 ILE cc_start: 0.8123 (mm) cc_final: 0.7839 (pt) REVERT: A 175 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8191 (tpt170) REVERT: B 72 MET cc_start: 0.9251 (mtt) cc_final: 0.8593 (tpt) REVERT: B 137 MET cc_start: 0.6486 (ppp) cc_final: 0.6006 (ppp) REVERT: D 133 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7722 (mtt180) REVERT: K 2152 ASP cc_start: 0.7824 (m-30) cc_final: 0.7208 (t70) REVERT: K 2155 GLN cc_start: 0.8263 (tt0) cc_final: 0.8033 (tp40) REVERT: K 2156 LEU cc_start: 0.9172 (tt) cc_final: 0.8633 (tt) REVERT: K 2179 ASP cc_start: 0.9277 (t0) cc_final: 0.8788 (t0) REVERT: K 2256 MET cc_start: 0.5272 (ptm) cc_final: 0.4741 (ptp) REVERT: K 2257 ASN cc_start: 0.5983 (t0) cc_final: 0.5605 (m110) REVERT: N 175 CYS cc_start: 0.8630 (m) cc_final: 0.8244 (p) REVERT: N 186 GLU cc_start: 0.8386 (mp0) cc_final: 0.7980 (mp0) REVERT: N 269 TRP cc_start: 0.8361 (m100) cc_final: 0.7890 (m100) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.2821 time to fit residues: 58.2362 Evaluate side-chains 119 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.091471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.076458 restraints weight = 86223.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.078145 restraints weight = 59546.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.078675 restraints weight = 41937.083| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9762 Z= 0.235 Angle : 0.736 10.013 13171 Z= 0.386 Chirality : 0.045 0.217 1452 Planarity : 0.005 0.075 1709 Dihedral : 4.477 30.325 1258 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 0.09 % Allowed : 1.12 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1155 helix: 1.07 (0.18), residues: 758 sheet: -1.28 (0.56), residues: 81 loop : -0.74 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 4 190 HIS 0.006 0.001 HIS 4 164 PHE 0.047 0.003 PHE B 80 TYR 0.022 0.002 TYR 4 153 ARG 0.010 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.166 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: 4 159 MET cc_start: 0.8212 (ppp) cc_final: 0.7131 (ppp) REVERT: 4 180 LEU cc_start: 0.7940 (tp) cc_final: 0.7442 (tp) REVERT: 5 131 LEU cc_start: 0.9050 (mt) cc_final: 0.8795 (pp) REVERT: A 79 PHE cc_start: 0.8982 (m-80) cc_final: 0.8625 (m-80) REVERT: A 93 ILE cc_start: 0.8376 (mm) cc_final: 0.7915 (pt) REVERT: A 175 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8406 (mmm160) REVERT: B 41 MET cc_start: 0.0195 (ppp) cc_final: -0.0097 (ppp) REVERT: B 72 MET cc_start: 0.9168 (mtt) cc_final: 0.8514 (tpt) REVERT: B 137 MET cc_start: 0.6603 (ppp) cc_final: 0.6066 (ppp) REVERT: D 133 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7791 (mtt180) REVERT: D 231 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8500 (t70) REVERT: D 266 GLU cc_start: 0.8957 (mp0) cc_final: 0.8525 (pm20) REVERT: K 2179 ASP cc_start: 0.9393 (t0) cc_final: 0.8683 (t0) REVERT: K 2181 ASN cc_start: 0.7696 (p0) cc_final: 0.7210 (p0) REVERT: K 2256 MET cc_start: 0.6303 (ptm) cc_final: 0.5842 (mtt) REVERT: K 2281 THR cc_start: 0.8528 (p) cc_final: 0.8324 (p) REVERT: K 2293 LEU cc_start: 0.6968 (mt) cc_final: 0.6532 (mt) REVERT: K 2325 ASN cc_start: 0.8557 (t0) cc_final: 0.8275 (t0) REVERT: K 2336 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8037 (tm-30) REVERT: N 175 CYS cc_start: 0.8898 (m) cc_final: 0.8358 (p) REVERT: N 269 TRP cc_start: 0.8530 (m100) cc_final: 0.7849 (m100) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.2698 time to fit residues: 51.7167 Evaluate side-chains 109 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN B 155 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.088762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.073526 restraints weight = 87276.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.075086 restraints weight = 58558.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.075962 restraints weight = 43965.627| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.8191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9762 Z= 0.262 Angle : 0.766 12.804 13171 Z= 0.393 Chirality : 0.046 0.225 1452 Planarity : 0.005 0.064 1709 Dihedral : 4.746 30.124 1258 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1155 helix: 0.89 (0.18), residues: 755 sheet: -1.36 (0.56), residues: 83 loop : -0.89 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K2140 HIS 0.008 0.001 HIS B 191 PHE 0.034 0.002 PHE A 28 TYR 0.022 0.002 TYR 4 153 ARG 0.008 0.001 ARG 5 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.024 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: 4 159 MET cc_start: 0.8594 (ppp) cc_final: 0.7425 (ppp) REVERT: 5 131 LEU cc_start: 0.9071 (mt) cc_final: 0.8809 (pp) REVERT: 5 171 MET cc_start: 0.5297 (mmp) cc_final: 0.5059 (mmm) REVERT: A 79 PHE cc_start: 0.9146 (m-80) cc_final: 0.8609 (m-80) REVERT: A 82 MET cc_start: 0.2155 (mmm) cc_final: 0.1761 (mmm) REVERT: A 93 ILE cc_start: 0.8860 (mm) cc_final: 0.8431 (pt) REVERT: A 156 LEU cc_start: 0.9283 (mt) cc_final: 0.8922 (pp) REVERT: A 175 ARG cc_start: 0.8369 (mmm160) cc_final: 0.7879 (mmt180) REVERT: B 41 MET cc_start: 0.0690 (ppp) cc_final: 0.0449 (ppp) REVERT: B 72 MET cc_start: 0.9299 (mtt) cc_final: 0.8673 (tpt) REVERT: B 119 LYS cc_start: 0.3267 (mmpt) cc_final: 0.3024 (mmpt) REVERT: B 137 MET cc_start: 0.6642 (ppp) cc_final: 0.6138 (ppp) REVERT: B 195 ARG cc_start: 0.8763 (mmt180) cc_final: 0.8507 (mmt180) REVERT: D 266 GLU cc_start: 0.8966 (mp0) cc_final: 0.8623 (pm20) REVERT: D 311 GLN cc_start: 0.9149 (tt0) cc_final: 0.8711 (tm-30) REVERT: K 2179 ASP cc_start: 0.9534 (t0) cc_final: 0.8757 (t0) REVERT: K 2181 ASN cc_start: 0.7786 (p0) cc_final: 0.7273 (p0) REVERT: K 2281 THR cc_start: 0.8560 (p) cc_final: 0.8334 (p) REVERT: K 2293 LEU cc_start: 0.7255 (mt) cc_final: 0.6794 (mt) REVERT: N 175 CYS cc_start: 0.8944 (m) cc_final: 0.8428 (p) REVERT: N 269 TRP cc_start: 0.8590 (m100) cc_final: 0.7884 (m100) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2562 time to fit residues: 46.8363 Evaluate side-chains 104 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 0.0370 chunk 53 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.090120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.074869 restraints weight = 86927.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.076506 restraints weight = 57577.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.077468 restraints weight = 42456.693| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.8286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9762 Z= 0.192 Angle : 0.740 12.413 13171 Z= 0.378 Chirality : 0.045 0.252 1452 Planarity : 0.005 0.061 1709 Dihedral : 4.657 29.176 1258 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1155 helix: 0.99 (0.18), residues: 753 sheet: -1.34 (0.59), residues: 75 loop : -0.85 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K2140 HIS 0.007 0.001 HIS B 191 PHE 0.027 0.002 PHE B 80 TYR 0.033 0.001 TYR A 31 ARG 0.009 0.001 ARG N 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.220 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: 4 159 MET cc_start: 0.8676 (ppp) cc_final: 0.7393 (ppp) REVERT: 4 180 LEU cc_start: 0.7939 (tp) cc_final: 0.7654 (tp) REVERT: 5 131 LEU cc_start: 0.9016 (mt) cc_final: 0.8773 (pp) REVERT: A 79 PHE cc_start: 0.9078 (m-80) cc_final: 0.8482 (m-80) REVERT: A 156 LEU cc_start: 0.9252 (mt) cc_final: 0.8926 (pp) REVERT: A 175 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7811 (mmm160) REVERT: B 72 MET cc_start: 0.9283 (mtt) cc_final: 0.8663 (tpt) REVERT: B 119 LYS cc_start: 0.3316 (mmpt) cc_final: 0.3036 (mmpt) REVERT: B 137 MET cc_start: 0.6534 (ppp) cc_final: 0.6039 (ppp) REVERT: D 133 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7561 (mtt180) REVERT: D 266 GLU cc_start: 0.8921 (mp0) cc_final: 0.8592 (pm20) REVERT: D 311 GLN cc_start: 0.9019 (tt0) cc_final: 0.8766 (tm-30) REVERT: K 2152 ASP cc_start: 0.7650 (m-30) cc_final: 0.6737 (t70) REVERT: K 2179 ASP cc_start: 0.9396 (t0) cc_final: 0.8656 (t0) REVERT: K 2181 ASN cc_start: 0.7690 (p0) cc_final: 0.7055 (p0) REVERT: K 2201 LEU cc_start: 0.8985 (mt) cc_final: 0.8689 (pp) REVERT: K 2227 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8530 (tp30) REVERT: K 2281 THR cc_start: 0.8641 (p) cc_final: 0.7818 (p) REVERT: N 175 CYS cc_start: 0.8883 (m) cc_final: 0.8349 (p) REVERT: N 269 TRP cc_start: 0.8500 (m100) cc_final: 0.7806 (m100) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2589 time to fit residues: 49.9740 Evaluate side-chains 114 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.089713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.074530 restraints weight = 86742.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.075995 restraints weight = 58752.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.077136 restraints weight = 43691.593| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9762 Z= 0.192 Angle : 0.728 12.184 13171 Z= 0.370 Chirality : 0.044 0.251 1452 Planarity : 0.004 0.061 1709 Dihedral : 4.659 29.165 1258 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1155 helix: 1.07 (0.18), residues: 758 sheet: -1.31 (0.58), residues: 75 loop : -0.80 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K2249 HIS 0.006 0.001 HIS 4 174 PHE 0.027 0.002 PHE A 28 TYR 0.011 0.001 TYR 4 153 ARG 0.007 0.001 ARG B 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.77 seconds wall clock time: 84 minutes 50.87 seconds (5090.87 seconds total)