Starting phenix.real_space_refine on Fri Mar 14 04:40:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q5h_18179/03_2025/8q5h_18179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q5h_18179/03_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_18179/03_2025/8q5h_18179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q5h_18179/03_2025/8q5h_18179.map" model { file = "/net/cci-nas-00/data/ceres_data/8q5h_18179/03_2025/8q5h_18179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q5h_18179/03_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-5624/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: 5.96, per 1000 atoms: 0.62 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: 2.32 Conformation dependent library (CDL) restraints added in 1.5 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: 0.89 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: 2.84 Time building geometry restraints manager: 2.76 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.250 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:3.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- 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 : 1.110 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: 0.2976 time to fit residues: 100.7034 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 : 1.033 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.085482 restraints weight = 79879.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.087142 restraints weight = 53222.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.088427 restraints weight = 39321.004| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 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 : 1.040 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: 0.5334 (ppp) cc_final: 0.4399 (ppp) REVERT: 5 171 MET cc_start: 0.4840 (mmp) cc_final: 0.4550 (mmp) REVERT: 5 197 PHE cc_start: 0.7608 (m-10) cc_final: 0.7282 (m-10) REVERT: 5 199 GLU cc_start: 0.8861 (tp30) cc_final: 0.8648 (tm-30) REVERT: A 61 ARG cc_start: 0.8665 (tpt170) cc_final: 0.8440 (tpt170) REVERT: A 145 GLN cc_start: 0.8995 (mt0) cc_final: 0.8065 (mt0) REVERT: B 72 MET cc_start: 0.9373 (mtt) cc_final: 0.8725 (tpt) REVERT: D 270 THR cc_start: 0.8758 (t) cc_final: 0.8400 (p) REVERT: D 325 MET cc_start: 0.8096 (mmm) cc_final: 0.7756 (mmm) REVERT: K 2155 GLN cc_start: 0.8096 (tt0) cc_final: 0.7611 (tp-100) REVERT: K 2156 LEU cc_start: 0.8316 (tt) cc_final: 0.7826 (tt) REVERT: K 2179 ASP cc_start: 0.9107 (t0) cc_final: 0.8271 (t0) REVERT: K 2181 ASN cc_start: 0.7358 (p0) cc_final: 0.6287 (p0) REVERT: K 2241 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7072 (pt0) REVERT: K 2256 MET cc_start: 0.3375 (ptm) cc_final: 0.2908 (ptp) REVERT: N 175 CYS cc_start: 0.8538 (m) cc_final: 0.8108 (p) REVERT: N 269 TRP cc_start: 0.8161 (m100) cc_final: 0.7702 (m100) outliers start: 4 outliers final: 0 residues processed: 176 average time/residue: 0.2815 time to fit residues: 64.5826 Evaluate side-chains 122 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** D 314 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 = 0.4453 r_free = 0.4453 target = 0.099762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.084470 restraints weight = 81713.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.086084 restraints weight = 55612.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.087304 restraints weight = 41503.988| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9762 Z= 0.177 Angle : 0.645 11.796 13171 Z= 0.328 Chirality : 0.042 0.159 1452 Planarity : 0.005 0.051 1709 Dihedral : 4.352 31.725 1258 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 1.42 (0.18), residues: 748 sheet: -1.84 (0.59), residues: 75 loop : -0.86 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K2249 HIS 0.005 0.001 HIS N 217 PHE 0.029 0.002 PHE N 115 TYR 0.012 0.001 TYR K2331 ARG 0.016 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 161 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.026 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: 0.7150 (ppp) cc_final: 0.6269 (ppp) REVERT: 4 180 LEU cc_start: 0.6720 (tp) cc_final: 0.6092 (tt) REVERT: 5 199 GLU cc_start: 0.8858 (tp30) cc_final: 0.8653 (tm-30) REVERT: A 79 PHE cc_start: 0.8907 (m-80) cc_final: 0.8425 (m-80) REVERT: A 175 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7357 (mmm160) REVERT: B 41 MET cc_start: 0.0607 (ppp) cc_final: 0.0267 (ppp) REVERT: B 72 MET cc_start: 0.9380 (mtt) cc_final: 0.8694 (tpt) REVERT: D 126 VAL cc_start: 0.7055 (t) cc_final: 0.6817 (t) REVERT: D 270 THR cc_start: 0.8880 (t) cc_final: 0.8507 (p) REVERT: K 2152 ASP cc_start: 0.7838 (m-30) cc_final: 0.7189 (t70) REVERT: K 2155 GLN cc_start: 0.8190 (tt0) cc_final: 0.7858 (tp-100) REVERT: K 2156 LEU cc_start: 0.8405 (tt) cc_final: 0.7898 (tt) REVERT: K 2179 ASP cc_start: 0.9133 (t0) cc_final: 0.8624 (t0) REVERT: K 2236 CYS cc_start: 0.8027 (m) cc_final: 0.6712 (t) REVERT: K 2241 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7250 (pt0) REVERT: N 175 CYS cc_start: 0.8551 (m) cc_final: 0.8130 (p) REVERT: N 269 TRP cc_start: 0.8217 (m100) cc_final: 0.7712 (m100) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2507 time to fit residues: 54.1274 Evaluate side-chains 126 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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: 6.9990 chunk 77 optimal weight: 0.0040 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN D 231 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.098450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.083251 restraints weight = 81134.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.084953 restraints weight = 55352.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.086122 restraints weight = 41208.178| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9762 Z= 0.170 Angle : 0.650 10.109 13171 Z= 0.332 Chirality : 0.042 0.162 1452 Planarity : 0.004 0.043 1709 Dihedral : 4.312 31.401 1258 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % 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: 0.81 (0.25), residues: 1155 helix: 1.43 (0.18), residues: 750 sheet: -1.89 (0.55), residues: 80 loop : -0.82 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K2249 HIS 0.004 0.001 HIS B 134 PHE 0.024 0.002 PHE N 115 TYR 0.018 0.001 TYR A 31 ARG 0.009 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 155 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.144 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: 0.7377 (ppp) cc_final: 0.6476 (ppp) REVERT: 4 180 LEU cc_start: 0.7239 (tp) cc_final: 0.6728 (tt) REVERT: 5 131 LEU cc_start: 0.8167 (mp) cc_final: 0.7954 (pp) REVERT: 5 199 GLU cc_start: 0.8837 (tp30) cc_final: 0.8636 (tm-30) REVERT: A 79 PHE cc_start: 0.8973 (m-80) cc_final: 0.8586 (m-80) REVERT: A 175 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7701 (tpt170) REVERT: B 41 MET cc_start: 0.0054 (ppp) cc_final: -0.0317 (ppp) REVERT: B 72 MET cc_start: 0.9323 (mtt) cc_final: 0.8617 (tpt) REVERT: B 190 LEU cc_start: 0.9188 (mp) cc_final: 0.8609 (mp) REVERT: D 133 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7309 (mtt90) REVERT: D 292 MET cc_start: 0.8069 (tmm) cc_final: 0.6909 (ppp) REVERT: K 2155 GLN cc_start: 0.8130 (tt0) cc_final: 0.7920 (tp40) REVERT: K 2156 LEU cc_start: 0.8419 (tt) cc_final: 0.7927 (tt) REVERT: K 2179 ASP cc_start: 0.9174 (t0) cc_final: 0.8687 (t0) REVERT: K 2239 LEU cc_start: 0.9010 (tp) cc_final: 0.8669 (tt) REVERT: K 2241 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7582 (pt0) REVERT: N 175 CYS cc_start: 0.8661 (m) cc_final: 0.8178 (p) REVERT: N 269 TRP cc_start: 0.8183 (m100) cc_final: 0.7642 (m100) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2591 time to fit residues: 53.6273 Evaluate side-chains 119 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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: 0.8980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.082297 restraints weight = 81738.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.084011 restraints weight = 55379.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.085111 restraints weight = 41333.070| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5269 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= 0.171 Angle : 0.638 9.530 13171 Z= 0.327 Chirality : 0.042 0.148 1452 Planarity : 0.004 0.049 1709 Dihedral : 4.299 31.700 1258 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % 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: 0.87 (0.25), residues: 1155 helix: 1.48 (0.18), residues: 749 sheet: -1.81 (0.56), residues: 80 loop : -0.81 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K2249 HIS 0.004 0.001 HIS K2234 PHE 0.020 0.002 PHE 5 172 TYR 0.013 0.001 TYR B 77 ARG 0.009 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 152 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.077 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: 4 159 MET cc_start: 0.7487 (ppp) cc_final: 0.6586 (ppp) REVERT: 4 180 LEU cc_start: 0.7481 (tp) cc_final: 0.6991 (tt) REVERT: A 79 PHE cc_start: 0.8680 (m-80) cc_final: 0.8408 (m-80) REVERT: A 175 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7837 (mmm160) REVERT: B 72 MET cc_start: 0.9302 (mtt) cc_final: 0.8673 (tpt) REVERT: D 133 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7336 (mtt90) REVERT: D 292 MET cc_start: 0.8153 (tmm) cc_final: 0.7913 (ppp) REVERT: K 2152 ASP cc_start: 0.7824 (m-30) cc_final: 0.7120 (t70) REVERT: K 2155 GLN cc_start: 0.8238 (tt0) cc_final: 0.7995 (tp40) REVERT: K 2156 LEU cc_start: 0.8671 (tt) cc_final: 0.8012 (tt) REVERT: K 2167 PHE cc_start: 0.6113 (p90) cc_final: 0.5900 (p90) REVERT: K 2175 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6242 (mmm160) REVERT: K 2179 ASP cc_start: 0.9151 (t0) cc_final: 0.8492 (t0) REVERT: K 2181 ASN cc_start: 0.7716 (p0) cc_final: 0.6848 (p0) REVERT: K 2256 MET cc_start: 0.5171 (ptm) cc_final: 0.4678 (ptp) REVERT: K 2328 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7971 (ttmt) REVERT: N 175 CYS cc_start: 0.8715 (m) cc_final: 0.8275 (p) REVERT: N 269 TRP cc_start: 0.8387 (m100) cc_final: 0.7910 (m100) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2578 time to fit residues: 53.1453 Evaluate side-chains 117 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 42 optimal weight: 0.0070 chunk 73 optimal weight: 0.2980 chunk 108 optimal weight: 0.0040 overall best weight: 0.3810 ------------------------------------------------------------------------------- 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2325 ASN ** 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 = 0.4423 r_free = 0.4423 target = 0.097711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.082560 restraints weight = 82188.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.084251 restraints weight = 55798.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.085438 restraints weight = 41339.928| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.5583 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= 0.165 Angle : 0.652 9.531 13171 Z= 0.335 Chirality : 0.042 0.146 1452 Planarity : 0.004 0.040 1709 Dihedral : 4.328 30.605 1258 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 0.28 % Allowed : 2.71 % Favored : 97.01 % 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: 1.48 (0.18), residues: 751 sheet: -1.64 (0.57), residues: 80 loop : -0.77 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K2249 HIS 0.012 0.001 HIS B 191 PHE 0.023 0.002 PHE 5 172 TYR 0.011 0.001 TYR B 77 ARG 0.009 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 148 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 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: 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: 0.7564 (ppp) cc_final: 0.6643 (ppp) REVERT: 4 180 LEU cc_start: 0.7505 (tp) cc_final: 0.7183 (tp) REVERT: A 79 PHE cc_start: 0.8766 (m-80) cc_final: 0.8453 (m-80) REVERT: B 72 MET cc_start: 0.9286 (mtt) cc_final: 0.8595 (tpt) REVERT: B 137 MET cc_start: 0.6250 (ppp) cc_final: 0.5949 (ppp) REVERT: D 231 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.8223 (t70) REVERT: D 270 THR cc_start: 0.8873 (t) cc_final: 0.8501 (p) REVERT: D 325 MET cc_start: 0.8075 (mmm) cc_final: 0.7843 (mmt) REVERT: K 2152 ASP cc_start: 0.7708 (m-30) cc_final: 0.7056 (t70) REVERT: K 2155 GLN cc_start: 0.8120 (tt0) cc_final: 0.7829 (tt0) REVERT: K 2175 ARG cc_start: 0.6630 (ttt180) cc_final: 0.6022 (mmm160) REVERT: K 2179 ASP cc_start: 0.9206 (t0) cc_final: 0.8504 (t0) REVERT: K 2181 ASN cc_start: 0.7655 (p0) cc_final: 0.6696 (p0) REVERT: K 2256 MET cc_start: 0.5129 (ptm) cc_final: 0.4669 (ptp) REVERT: K 2328 LYS cc_start: 0.8250 (ttpp) cc_final: 0.8022 (ttmt) REVERT: N 175 CYS cc_start: 0.8693 (m) cc_final: 0.8256 (p) REVERT: N 269 TRP cc_start: 0.8202 (m100) cc_final: 0.7755 (m100) outliers start: 3 outliers final: 1 residues processed: 147 average time/residue: 0.2540 time to fit residues: 50.7216 Evaluate side-chains 111 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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: 0.1980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 20 optimal weight: 0.0870 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- 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 153 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2332 GLN K2336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.097955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.083030 restraints weight = 82067.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.084587 restraints weight = 56109.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.085884 restraints weight = 41560.410| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.5880 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= 0.163 Angle : 0.659 10.688 13171 Z= 0.339 Chirality : 0.043 0.145 1452 Planarity : 0.004 0.044 1709 Dihedral : 4.303 30.498 1258 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 0.19 % Allowed : 1.49 % Favored : 98.32 % 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: 1.39 (0.18), residues: 753 sheet: -1.50 (0.58), residues: 77 loop : -0.78 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 78 HIS 0.007 0.001 HIS B 191 PHE 0.020 0.001 PHE 5 172 TYR 0.011 0.001 TYR B 62 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 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 1.022 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: 0.7367 (ppp) cc_final: 0.6451 (ppp) REVERT: 4 180 LEU cc_start: 0.7530 (tp) cc_final: 0.7204 (tp) REVERT: 5 131 LEU cc_start: 0.8573 (mm) cc_final: 0.8173 (pp) REVERT: A 79 PHE cc_start: 0.8730 (m-80) cc_final: 0.8302 (m-80) REVERT: A 175 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7625 (mmm160) REVERT: B 72 MET cc_start: 0.9265 (mtt) cc_final: 0.8592 (tpt) REVERT: B 137 MET cc_start: 0.6237 (ppp) cc_final: 0.5820 (ppp) REVERT: D 133 ARG cc_start: 0.8356 (mmm160) cc_final: 0.7598 (mtt180) REVERT: D 325 MET cc_start: 0.8092 (mmm) cc_final: 0.7768 (mmt) REVERT: K 2152 ASP cc_start: 0.7775 (m-30) cc_final: 0.7134 (t70) REVERT: K 2155 GLN cc_start: 0.8109 (tt0) cc_final: 0.7874 (tp40) REVERT: K 2156 LEU cc_start: 0.9011 (tt) cc_final: 0.8469 (tt) REVERT: K 2179 ASP cc_start: 0.9219 (t0) cc_final: 0.8930 (t0) REVERT: K 2256 MET cc_start: 0.5126 (ptm) cc_final: 0.4719 (ptp) REVERT: K 2328 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7993 (ttmt) REVERT: N 175 CYS cc_start: 0.8640 (m) cc_final: 0.8225 (p) REVERT: N 186 GLU cc_start: 0.8303 (mp0) cc_final: 0.7949 (mp0) REVERT: N 269 TRP cc_start: 0.8256 (m100) cc_final: 0.7790 (m100) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.2393 time to fit residues: 48.7810 Evaluate side-chains 116 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 184 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2325 ASN ** 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 = 0.4388 r_free = 0.4388 target = 0.095808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.080867 restraints weight = 84760.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.082571 restraints weight = 60127.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.083936 restraints weight = 40393.620| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9762 Z= 0.189 Angle : 0.677 10.528 13171 Z= 0.350 Chirality : 0.043 0.147 1452 Planarity : 0.004 0.039 1709 Dihedral : 4.324 30.401 1258 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.39 (0.18), residues: 758 sheet: -1.52 (0.55), residues: 82 loop : -0.79 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 78 HIS 0.004 0.001 HIS B 191 PHE 0.034 0.002 PHE B 80 TYR 0.013 0.001 TYR K2174 ARG 0.011 0.001 ARG N 37 *********************** 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 144 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.033 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: 0.7626 (ppp) cc_final: 0.6618 (ppp) REVERT: 4 180 LEU cc_start: 0.7681 (tp) cc_final: 0.7334 (tp) REVERT: 5 131 LEU cc_start: 0.8629 (mm) cc_final: 0.8203 (pp) REVERT: A 71 MET cc_start: 0.8220 (mpp) cc_final: 0.7985 (mpp) REVERT: A 79 PHE cc_start: 0.8896 (m-80) cc_final: 0.8596 (m-80) REVERT: A 93 ILE cc_start: 0.7944 (mm) cc_final: 0.7596 (pt) REVERT: A 192 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8044 (ttm170) REVERT: B 72 MET cc_start: 0.9271 (mtt) cc_final: 0.8597 (tpt) REVERT: B 137 MET cc_start: 0.6302 (ppp) cc_final: 0.5912 (ppp) REVERT: D 133 ARG cc_start: 0.8506 (mmm160) cc_final: 0.7753 (mtt180) REVERT: D 325 MET cc_start: 0.8133 (mmm) cc_final: 0.7855 (mmt) REVERT: K 2152 ASP cc_start: 0.7779 (m-30) cc_final: 0.7143 (t70) REVERT: K 2155 GLN cc_start: 0.8267 (tt0) cc_final: 0.8013 (tp40) REVERT: K 2156 LEU cc_start: 0.8981 (tt) cc_final: 0.8458 (tt) REVERT: K 2179 ASP cc_start: 0.9359 (t0) cc_final: 0.8758 (t0) REVERT: K 2181 ASN cc_start: 0.8814 (t0) cc_final: 0.8127 (p0) REVERT: K 2256 MET cc_start: 0.5490 (ptm) cc_final: 0.4894 (ptp) REVERT: K 2328 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8203 (ttmt) REVERT: N 175 CYS cc_start: 0.8722 (m) cc_final: 0.8300 (p) REVERT: N 269 TRP cc_start: 0.8143 (m100) cc_final: 0.7718 (m100) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2396 time to fit residues: 47.9423 Evaluate side-chains 118 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 20 optimal weight: 0.0060 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K2336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.095501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.080757 restraints weight = 83665.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.082467 restraints weight = 59327.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.084135 restraints weight = 39499.063| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.6806 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= 0.175 Angle : 0.667 10.240 13171 Z= 0.346 Chirality : 0.043 0.221 1452 Planarity : 0.004 0.041 1709 Dihedral : 4.357 31.588 1258 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 0.09 % Allowed : 0.65 % Favored : 99.25 % 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: 1.37 (0.18), residues: 762 sheet: -1.43 (0.55), residues: 83 loop : -0.78 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K2249 HIS 0.004 0.001 HIS K2199 PHE 0.035 0.002 PHE B 80 TYR 0.012 0.001 TYR K2245 ARG 0.008 0.001 ARG N 37 *********************** 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 143 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.066 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: 4 159 MET cc_start: 0.7803 (ppp) cc_final: 0.6792 (ppp) REVERT: 4 180 LEU cc_start: 0.7714 (tp) cc_final: 0.7407 (tp) REVERT: 5 131 LEU cc_start: 0.8619 (mm) cc_final: 0.8215 (pp) REVERT: A 79 PHE cc_start: 0.8882 (m-80) cc_final: 0.8406 (m-80) REVERT: A 82 MET cc_start: 0.0431 (mmm) cc_final: 0.0073 (mmm) REVERT: A 93 ILE cc_start: 0.8064 (mm) cc_final: 0.7756 (pt) REVERT: B 72 MET cc_start: 0.9309 (mtt) cc_final: 0.8695 (tpt) REVERT: B 137 MET cc_start: 0.6351 (ppp) cc_final: 0.5923 (ppp) REVERT: B 192 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.6804 (mpt180) REVERT: B 195 ARG cc_start: 0.8671 (mmt180) cc_final: 0.8351 (mtp180) REVERT: D 133 ARG cc_start: 0.8494 (mmm160) cc_final: 0.7772 (mtt180) REVERT: K 2152 ASP cc_start: 0.8064 (m-30) cc_final: 0.7242 (t70) REVERT: K 2156 LEU cc_start: 0.8954 (tt) cc_final: 0.8395 (tt) REVERT: K 2179 ASP cc_start: 0.9355 (t0) cc_final: 0.8955 (t0) REVERT: K 2181 ASN cc_start: 0.8845 (t0) cc_final: 0.8362 (p0) REVERT: K 2256 MET cc_start: 0.5411 (ptm) cc_final: 0.4924 (ptp) REVERT: K 2325 ASN cc_start: 0.8328 (t0) cc_final: 0.8020 (t0) REVERT: K 2328 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8115 (ttmt) REVERT: K 2337 ASP cc_start: 0.8801 (m-30) cc_final: 0.8577 (m-30) REVERT: N 175 CYS cc_start: 0.8734 (m) cc_final: 0.8227 (p) REVERT: N 186 GLU cc_start: 0.8480 (mp0) cc_final: 0.8117 (mp0) REVERT: N 269 TRP cc_start: 0.8189 (m100) cc_final: 0.7769 (m100) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.2547 time to fit residues: 49.1789 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 : 1.094 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.0030 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 189 GLN B 83 GLN ** 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** ** K2199 HIS ** 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 = 0.4390 r_free = 0.4390 target = 0.095573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.080661 restraints weight = 84413.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.082520 restraints weight = 59692.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.083877 restraints weight = 39448.069| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9762 Z= 0.177 Angle : 0.683 10.046 13171 Z= 0.350 Chirality : 0.044 0.260 1452 Planarity : 0.005 0.079 1709 Dihedral : 4.381 29.989 1258 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.97 % 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 : 0.00 % 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: 0.83 (0.25), residues: 1155 helix: 1.35 (0.18), residues: 761 sheet: -1.48 (0.56), residues: 75 loop : -0.79 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 78 HIS 0.003 0.001 HIS B 134 PHE 0.044 0.002 PHE B 80 TYR 0.013 0.001 TYR K2245 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 146 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.162 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: 0.7807 (ppp) cc_final: 0.6758 (ppp) REVERT: 4 180 LEU cc_start: 0.7703 (tp) cc_final: 0.7388 (tp) REVERT: 5 131 LEU cc_start: 0.8730 (mm) cc_final: 0.8319 (pp) REVERT: A 21 MET cc_start: 0.8402 (ppp) cc_final: 0.8151 (ppp) REVERT: A 61 ARG cc_start: 0.8523 (tpt170) cc_final: 0.8317 (ttt180) REVERT: A 71 MET cc_start: 0.8063 (mpp) cc_final: 0.7847 (mpp) REVERT: A 79 PHE cc_start: 0.8904 (m-80) cc_final: 0.8423 (m-80) REVERT: A 93 ILE cc_start: 0.7995 (mm) cc_final: 0.7694 (pt) REVERT: A 175 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8152 (tpt170) REVERT: B 72 MET cc_start: 0.9286 (mtt) cc_final: 0.8679 (tpt) REVERT: B 137 MET cc_start: 0.6374 (ppp) cc_final: 0.5938 (ppp) REVERT: B 192 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.6764 (mpt180) REVERT: B 195 ARG cc_start: 0.8613 (mmt180) cc_final: 0.8238 (mtp180) REVERT: D 133 ARG cc_start: 0.8453 (mmm160) cc_final: 0.7751 (mtt180) REVERT: D 266 GLU cc_start: 0.8639 (mp0) cc_final: 0.8397 (pm20) REVERT: D 325 MET cc_start: 0.7698 (mmt) cc_final: 0.7213 (mmm) REVERT: K 2152 ASP cc_start: 0.8068 (m-30) cc_final: 0.7313 (t70) REVERT: K 2179 ASP cc_start: 0.9381 (t0) cc_final: 0.8982 (t0) REVERT: K 2181 ASN cc_start: 0.8763 (t0) cc_final: 0.8296 (p0) REVERT: K 2256 MET cc_start: 0.5733 (ptm) cc_final: 0.5212 (ptp) REVERT: K 2325 ASN cc_start: 0.8399 (t0) cc_final: 0.8122 (t0) REVERT: K 2328 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8257 (ttmt) REVERT: N 175 CYS cc_start: 0.8689 (m) cc_final: 0.8189 (p) REVERT: N 186 GLU cc_start: 0.8420 (mp0) cc_final: 0.8035 (mp0) REVERT: N 269 TRP cc_start: 0.8352 (m100) cc_final: 0.7915 (m100) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2599 time to fit residues: 51.3610 Evaluate side-chains 116 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** 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** ** 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 = 0.4377 r_free = 0.4377 target = 0.094546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.079407 restraints weight = 84748.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.081358 restraints weight = 61613.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.082019 restraints weight = 41538.298| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.7375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9762 Z= 0.181 Angle : 0.679 9.088 13171 Z= 0.348 Chirality : 0.043 0.262 1452 Planarity : 0.005 0.073 1709 Dihedral : 4.327 29.229 1258 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % 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: 0.79 (0.25), residues: 1155 helix: 1.32 (0.18), residues: 759 sheet: -1.50 (0.54), residues: 83 loop : -0.71 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K2249 HIS 0.004 0.001 HIS K2199 PHE 0.035 0.002 PHE B 80 TYR 0.017 0.001 TYR K2245 ARG 0.010 0.001 ARG N 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5029.24 seconds wall clock time: 89 minutes 7.84 seconds (5347.84 seconds total)