Starting phenix.real_space_refine on Sat Aug 23 10:04:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ppr_17814/08_2025/8ppr_17814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ppr_17814/08_2025/8ppr_17814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ppr_17814/08_2025/8ppr_17814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ppr_17814/08_2025/8ppr_17814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ppr_17814/08_2025/8ppr_17814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ppr_17814/08_2025/8ppr_17814.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 49 5.16 5 C 7187 2.51 5 N 1948 2.21 5 O 2170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11354 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain: "M" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1692 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "N" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1767 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Chain: "P" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1434 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "G" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 140} Chain: "K" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2048 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 236} Chain: "Z" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 336 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.23 Number of scatterers: 11354 At special positions: 0 Unit cell: (78.366, 106.959, 321.936, 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 49 16.00 O 2170 8.00 N 1948 7.00 C 7187 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: 1.03 Conformation dependent library (CDL) restraints added in 395.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 73.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.830A pdb=" N GLU D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 124 removed outlier: 3.878A pdb=" N ARG D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 153 Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 160 through 186 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.652A pdb=" N CYS D 191 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 246 removed outlier: 5.633A pdb=" N SER D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 204 " --> pdb=" O SER D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 264 through 270 Processing helix chain 'D' and resid 274 through 326 removed outlier: 3.527A pdb=" N LEU D 278 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 removed outlier: 3.746A pdb=" N LYS D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 14 Processing helix chain 'M' and resid 16 through 50 removed outlier: 3.593A pdb=" N CYS M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 89 Processing helix chain 'M' and resid 99 through 106 removed outlier: 4.626A pdb=" N CYS M 104 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU M 106 " --> pdb=" O LYS M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 169 removed outlier: 3.527A pdb=" N LYS M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS M 169 " --> pdb=" O VAL M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 205 Processing helix chain 'N' and resid 42 through 59 removed outlier: 3.774A pdb=" N VAL N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG N 55 " --> pdb=" O GLN N 51 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE N 56 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 57 " --> pdb=" O CYS N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 63 Processing helix chain 'N' and resid 65 through 68 Processing helix chain 'N' and resid 69 through 86 removed outlier: 3.602A pdb=" N LEU N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 151 Proline residue: N 130 - end of helix Processing helix chain 'N' and resid 166 through 213 Proline residue: N 192 - end of helix Proline residue: N 209 - end of helix Processing helix chain 'N' and resid 214 through 221 Processing helix chain 'N' and resid 264 through 269 Processing helix chain 'P' and resid 33 through 53 Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 62 through 67 Processing helix chain 'P' and resid 69 through 99 Processing helix chain 'P' and resid 100 through 115 Processing helix chain 'P' and resid 128 through 189 removed outlier: 4.002A pdb=" N SER P 135 " --> pdb=" O LYS P 131 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL P 136 " --> pdb=" O ASP P 132 " (cutoff:3.500A) Proline residue: P 139 - end of helix removed outlier: 3.516A pdb=" N GLN P 161 " --> pdb=" O ALA P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 201 removed outlier: 4.571A pdb=" N GLU P 193 " --> pdb=" O ALA P 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 148 Proline residue: F 134 - end of helix Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'G' and resid 81 through 143 Processing helix chain 'G' and resid 194 through 205 removed outlier: 3.620A pdb=" N GLN G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN G 200 " --> pdb=" O GLU G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 223 removed outlier: 3.517A pdb=" N TYR G 223 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 2098 through 2130 Processing helix chain 'K' and resid 2150 through 2152 No H-bonds generated for 'chain 'K' and resid 2150 through 2152' Processing helix chain 'K' and resid 2171 through 2175 removed outlier: 3.562A pdb=" N ARG K2175 " --> pdb=" O LYS K2172 " (cutoff:3.500A) Processing helix chain 'K' and resid 2192 through 2209 Processing helix chain 'K' and resid 2211 through 2216 Processing helix chain 'K' and resid 2220 through 2250 removed outlier: 4.618A pdb=" N LYS K2224 " --> pdb=" O HIS K2220 " (cutoff:3.500A) removed outlier: 3.746A 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: 3.708A pdb=" N ILE K2309 " --> pdb=" O SER K2305 " (cutoff:3.500A) Processing helix chain 'K' and resid 2321 through 2335 Processing helix chain 'K' and resid 2338 through 2342 removed outlier: 3.513A pdb=" N TYR K2341 " --> pdb=" O CYS K2338 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS K2342 " --> pdb=" O HIS K2339 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2338 through 2342' Processing helix chain 'Z' and resid 184 through 221 removed outlier: 3.609A pdb=" N GLN Z 207 " --> pdb=" O ARG Z 203 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG Z 208 " --> pdb=" O ASP Z 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR Z 209 " --> pdb=" O LYS Z 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 38 through 40 removed outlier: 6.545A pdb=" N VAL N 38 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 253 through 254 removed outlier: 3.620A pdb=" N MET N 254 " --> pdb=" O TRP K2140 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL K2137 " --> pdb=" O THR K2148 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR K2148 " --> pdb=" O VAL K2137 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU K2139 " --> pdb=" O VAL K2146 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN K2144 " --> pdb=" O SER K2141 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE K2154 " --> pdb=" O PHE K2149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 149 through 151 Processing sheet with id=AA4, first strand: chain 'G' and resid 145 through 149 Processing sheet with id=AA5, first strand: chain 'K' and resid 2255 through 2260 removed outlier: 5.529A pdb=" N LEU K2255 " --> pdb=" O SER K2270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER K2270 " --> pdb=" O LEU K2255 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN K2257 " --> pdb=" O LEU K2268 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU K2279 " --> pdb=" O ASN K2299 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN K2299 " --> pdb=" O GLU K2279 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR K2281 " --> pdb=" O ILE K2297 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE K2297 " --> pdb=" O THR K2281 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3040 1.33 - 1.45: 1879 1.45 - 1.57: 6558 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 11553 Sorted by residual: bond pdb=" CG LEU F 97 " pdb=" CD1 LEU F 97 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" C ILE F 133 " pdb=" N PRO F 134 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.38e-02 5.25e+03 4.89e+00 bond pdb=" CG LEU F 97 " pdb=" CD2 LEU F 97 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.30e+00 bond pdb=" CB MET D 292 " pdb=" CG MET D 292 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 bond pdb=" CG LEU G 96 " pdb=" CD2 LEU G 96 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15369 2.39 - 4.78: 167 4.78 - 7.17: 23 7.17 - 9.56: 3 9.56 - 11.95: 3 Bond angle restraints: 15565 Sorted by residual: angle pdb=" CD1 LEU F 97 " pdb=" CG LEU F 97 " pdb=" CD2 LEU F 97 " ideal model delta sigma weight residual 110.80 101.81 8.99 2.20e+00 2.07e-01 1.67e+01 angle pdb=" CB LEU F 97 " pdb=" CG LEU F 97 " pdb=" CD1 LEU F 97 " ideal model delta sigma weight residual 110.70 99.58 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C PHE D 305 " pdb=" N MET D 306 " pdb=" CA MET D 306 " ideal model delta sigma weight residual 120.72 114.80 5.92 1.67e+00 3.59e-01 1.26e+01 angle pdb=" CA LEU F 102 " pdb=" CB LEU F 102 " pdb=" CG LEU F 102 " ideal model delta sigma weight residual 116.30 128.25 -11.95 3.50e+00 8.16e-02 1.17e+01 angle pdb=" CB MET D 292 " pdb=" CG MET D 292 " pdb=" SD MET D 292 " ideal model delta sigma weight residual 112.70 103.29 9.41 3.00e+00 1.11e-01 9.85e+00 ... (remaining 15560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 6429 17.50 - 34.99: 606 34.99 - 52.49: 77 52.49 - 69.99: 28 69.99 - 87.48: 13 Dihedral angle restraints: 7153 sinusoidal: 3043 harmonic: 4110 Sorted by residual: dihedral pdb=" CA PHE K2149 " pdb=" C PHE K2149 " pdb=" N VAL K2150 " pdb=" CA VAL K2150 " ideal model delta harmonic sigma weight residual -180.00 -149.46 -30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA ASN K2262 " pdb=" C ASN K2262 " pdb=" N ASN K2263 " pdb=" CA ASN K2263 " ideal model delta harmonic sigma weight residual -180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ASP N 253 " pdb=" C ASP N 253 " pdb=" N MET N 254 " pdb=" CA MET N 254 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 7150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1196 0.032 - 0.064: 344 0.064 - 0.096: 131 0.096 - 0.129: 41 0.129 - 0.161: 14 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CB ILE P 32 " pdb=" CA ILE P 32 " pdb=" CG1 ILE P 32 " pdb=" CG2 ILE P 32 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA GLU D 205 " pdb=" N GLU D 205 " pdb=" C GLU D 205 " pdb=" CB GLU D 205 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR P 31 " pdb=" CA THR P 31 " pdb=" OG1 THR P 31 " pdb=" CG2 THR P 31 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1723 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 133 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO F 134 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 134 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 134 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 67 " 0.017 2.00e-02 2.50e+03 1.68e-02 4.96e+00 pdb=" CG PHE M 67 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE M 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE M 67 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE M 67 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE M 67 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE M 67 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER M 56 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO M 57 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 57 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 57 " -0.028 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 187 2.69 - 3.24: 11725 3.24 - 3.79: 18813 3.79 - 4.35: 23420 4.35 - 4.90: 38297 Nonbonded interactions: 92442 Sorted by model distance: nonbonded pdb=" OG SER K2305 " pdb=" OD1 ASP K2307 " model vdw 2.133 3.040 nonbonded pdb=" O ILE F 149 " pdb=" OH TYR G 138 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP F 117 " pdb=" NE2 GLN F 121 " model vdw 2.170 3.120 nonbonded pdb=" O ASP F 117 " pdb=" NE2 GLN F 121 " model vdw 2.179 3.120 nonbonded pdb=" OE1 GLU P 203 " pdb=" OH TYR K2245 " model vdw 2.184 3.040 ... (remaining 92437 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.970 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 11553 Z= 0.148 Angle : 0.630 11.952 15565 Z= 0.331 Chirality : 0.039 0.161 1726 Planarity : 0.005 0.074 2019 Dihedral : 14.029 87.483 4461 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.23), residues: 1370 helix: 2.98 (0.16), residues: 939 sheet: -1.10 (0.50), residues: 101 loop : 0.54 (0.40), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K2120 TYR 0.014 0.001 TYR G 110 PHE 0.039 0.002 PHE M 67 TRP 0.028 0.002 TRP K2140 HIS 0.007 0.001 HIS K2220 Details of bonding type rmsd covalent geometry : bond 0.00306 (11553) covalent geometry : angle 0.63041 (15565) hydrogen bonds : bond 0.10479 ( 843) hydrogen bonds : angle 4.89756 ( 2466) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: D 98 ARG cc_start: 0.6396 (ptm160) cc_final: 0.6041 (ptm160) REVERT: M 1 MET cc_start: 0.3264 (ppp) cc_final: 0.2093 (tpt) REVERT: M 88 GLN cc_start: 0.8986 (tp40) cc_final: 0.8748 (tp40) REVERT: M 92 ARG cc_start: 0.6757 (tpp-160) cc_final: 0.6254 (tpp80) REVERT: M 104 CYS cc_start: 0.9098 (m) cc_final: 0.8034 (t) REVERT: P 38 LEU cc_start: 0.7919 (tt) cc_final: 0.7661 (tt) REVERT: P 131 LYS cc_start: 0.8621 (mppt) cc_final: 0.8160 (tptt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5656 time to fit residues: 80.8796 Evaluate side-chains 91 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 GLN D 147 GLN D 231 HIS M 194 ASN P 106 ASN ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2221 GLN ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.186877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124837 restraints weight = 20059.598| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.58 r_work: 0.3529 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11553 Z= 0.189 Angle : 0.605 9.974 15565 Z= 0.314 Chirality : 0.041 0.183 1726 Planarity : 0.004 0.065 2019 Dihedral : 4.015 30.511 1489 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 7.32 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.23), residues: 1370 helix: 2.95 (0.16), residues: 941 sheet: -1.58 (0.48), residues: 104 loop : 0.50 (0.39), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 23 TYR 0.017 0.002 TYR P 77 PHE 0.026 0.002 PHE M 67 TRP 0.013 0.002 TRP N 78 HIS 0.007 0.002 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00441 (11553) covalent geometry : angle 0.60457 (15565) hydrogen bonds : bond 0.04707 ( 843) hydrogen bonds : angle 4.18046 ( 2466) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: M 1 MET cc_start: 0.3440 (ppp) cc_final: 0.2312 (tpt) REVERT: M 25 TYR cc_start: 0.8537 (t80) cc_final: 0.8062 (t80) REVERT: M 70 PHE cc_start: 0.7809 (t80) cc_final: 0.7276 (t80) REVERT: M 74 HIS cc_start: 0.8054 (m90) cc_final: 0.7834 (m90) REVERT: M 88 GLN cc_start: 0.9054 (tp40) cc_final: 0.8817 (tp40) REVERT: M 104 CYS cc_start: 0.9388 (m) cc_final: 0.8558 (p) REVERT: P 130 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: G 152 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: K 2142 ASP cc_start: 0.7934 (m-30) cc_final: 0.7634 (m-30) REVERT: K 2225 MET cc_start: 0.8214 (tmm) cc_final: 0.7952 (tmm) outliers start: 21 outliers final: 4 residues processed: 117 average time/residue: 0.5791 time to fit residues: 73.1124 Evaluate side-chains 95 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 152 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 83 optimal weight: 50.0000 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 127 optimal weight: 0.0270 chunk 86 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS P 184 GLN ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 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 = 0.4646 r_free = 0.4646 target = 0.190042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.128436 restraints weight = 20318.701| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.65 r_work: 0.3559 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11553 Z= 0.125 Angle : 0.535 10.378 15565 Z= 0.275 Chirality : 0.038 0.185 1726 Planarity : 0.004 0.052 2019 Dihedral : 3.886 30.614 1489 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.65 % Allowed : 10.07 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.29 (0.23), residues: 1370 helix: 3.16 (0.16), residues: 938 sheet: -1.55 (0.47), residues: 102 loop : 0.52 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 23 TYR 0.018 0.001 TYR P 77 PHE 0.024 0.001 PHE M 86 TRP 0.011 0.001 TRP N 78 HIS 0.007 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00269 (11553) covalent geometry : angle 0.53518 (15565) hydrogen bonds : bond 0.04216 ( 843) hydrogen bonds : angle 3.83787 ( 2466) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3094 (ppp) cc_final: 0.2061 (tpt) REVERT: M 23 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7558 (ttp-170) REVERT: M 25 TYR cc_start: 0.8488 (t80) cc_final: 0.7995 (t80) REVERT: M 71 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: M 74 HIS cc_start: 0.8006 (m90) cc_final: 0.7756 (m90) REVERT: M 88 GLN cc_start: 0.8943 (tp40) cc_final: 0.8671 (tp40) REVERT: M 92 ARG cc_start: 0.7344 (tpp80) cc_final: 0.6922 (tpp80) REVERT: M 104 CYS cc_start: 0.9379 (m) cc_final: 0.8596 (p) REVERT: G 136 ASP cc_start: 0.8031 (t0) cc_final: 0.7692 (m-30) REVERT: G 152 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6747 (tt0) REVERT: K 2142 ASP cc_start: 0.7878 (m-30) cc_final: 0.7625 (m-30) REVERT: Z 212 PHE cc_start: 0.4482 (t80) cc_final: 0.4278 (t80) outliers start: 21 outliers final: 5 residues processed: 112 average time/residue: 0.5541 time to fit residues: 67.5797 Evaluate side-chains 96 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 94 optimal weight: 50.0000 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS M 11 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 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 = 0.4623 r_free = 0.4623 target = 0.188057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125657 restraints weight = 20319.512| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.65 r_work: 0.3525 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11553 Z= 0.155 Angle : 0.563 11.392 15565 Z= 0.286 Chirality : 0.039 0.190 1726 Planarity : 0.004 0.048 2019 Dihedral : 3.911 29.441 1489 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.12 % Allowed : 11.64 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.21 (0.23), residues: 1370 helix: 3.10 (0.16), residues: 940 sheet: -1.76 (0.47), residues: 102 loop : 0.55 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 23 TYR 0.019 0.001 TYR P 77 PHE 0.017 0.002 PHE G 210 TRP 0.011 0.001 TRP N 78 HIS 0.007 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00354 (11553) covalent geometry : angle 0.56350 (15565) hydrogen bonds : bond 0.04405 ( 843) hydrogen bonds : angle 3.88738 ( 2466) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3237 (ppp) cc_final: 0.1714 (tpt) REVERT: M 23 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7649 (ttp-170) REVERT: M 25 TYR cc_start: 0.8511 (t80) cc_final: 0.8013 (t80) REVERT: M 71 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7804 (mtp) REVERT: M 74 HIS cc_start: 0.8237 (m90) cc_final: 0.7998 (m90) REVERT: M 88 GLN cc_start: 0.8997 (tp40) cc_final: 0.8737 (tp40) REVERT: M 92 ARG cc_start: 0.7402 (tpp80) cc_final: 0.6810 (tpp80) REVERT: M 104 CYS cc_start: 0.9374 (m) cc_final: 0.8558 (p) REVERT: N 170 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7283 (mmm) REVERT: P 119 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6609 (tmmm) REVERT: P 130 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: K 2142 ASP cc_start: 0.7850 (m-30) cc_final: 0.7581 (m-30) outliers start: 27 outliers final: 8 residues processed: 111 average time/residue: 0.5664 time to fit residues: 68.2434 Evaluate side-chains 98 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS M 11 GLN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 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 = 0.4608 r_free = 0.4608 target = 0.186700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123549 restraints weight = 20166.014| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.63 r_work: 0.3487 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11553 Z= 0.203 Angle : 0.607 11.904 15565 Z= 0.310 Chirality : 0.041 0.181 1726 Planarity : 0.004 0.049 2019 Dihedral : 4.071 30.792 1489 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Rotamer: Outliers : 2.44 % Allowed : 12.51 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.23), residues: 1370 helix: 2.90 (0.16), residues: 932 sheet: -2.14 (0.45), residues: 104 loop : 0.44 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 97 TYR 0.020 0.002 TYR P 77 PHE 0.019 0.002 PHE G 210 TRP 0.012 0.002 TRP N 78 HIS 0.008 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00479 (11553) covalent geometry : angle 0.60724 (15565) hydrogen bonds : bond 0.04733 ( 843) hydrogen bonds : angle 4.00582 ( 2466) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3771 (ppp) cc_final: 0.2214 (tpt) REVERT: M 25 TYR cc_start: 0.8484 (t80) cc_final: 0.8020 (t80) REVERT: M 71 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7775 (mtp) REVERT: M 104 CYS cc_start: 0.9351 (m) cc_final: 0.8477 (p) REVERT: N 55 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6232 (mmp-170) REVERT: N 170 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7405 (mpp) REVERT: P 95 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.5121 (tp) REVERT: P 119 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6718 (tmmm) REVERT: P 130 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: K 2142 ASP cc_start: 0.7892 (m-30) cc_final: 0.7621 (m-30) REVERT: Z 214 GLN cc_start: 0.6165 (OUTLIER) cc_final: 0.5829 (tp40) outliers start: 31 outliers final: 9 residues processed: 114 average time/residue: 0.5811 time to fit residues: 71.2203 Evaluate side-chains 101 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2137 VAL Chi-restraints excluded: chain Z residue 214 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 129 optimal weight: 0.4980 chunk 50 optimal weight: 0.0060 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.0670 chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 120 optimal weight: 0.0970 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS Z 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.188871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.126812 restraints weight = 20168.381| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.64 r_work: 0.3540 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11553 Z= 0.127 Angle : 0.553 12.292 15565 Z= 0.283 Chirality : 0.038 0.194 1726 Planarity : 0.003 0.044 2019 Dihedral : 3.908 29.625 1489 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.97 % Allowed : 13.69 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.22 (0.23), residues: 1370 helix: 3.12 (0.16), residues: 941 sheet: -1.88 (0.47), residues: 102 loop : 0.52 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 23 TYR 0.020 0.001 TYR P 77 PHE 0.014 0.001 PHE M 79 TRP 0.007 0.001 TRP N 78 HIS 0.007 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00269 (11553) covalent geometry : angle 0.55350 (15565) hydrogen bonds : bond 0.04215 ( 843) hydrogen bonds : angle 3.81593 ( 2466) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3681 (ppp) cc_final: 0.2549 (tpt) REVERT: M 25 TYR cc_start: 0.8553 (t80) cc_final: 0.7992 (t80) REVERT: M 88 GLN cc_start: 0.8518 (tp40) cc_final: 0.8003 (pp30) REVERT: M 92 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.6835 (tpp-160) REVERT: M 104 CYS cc_start: 0.9386 (m) cc_final: 0.8615 (p) REVERT: N 55 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6313 (mmp-170) REVERT: N 170 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7305 (mmm) REVERT: P 119 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6654 (tmmm) REVERT: P 130 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: G 129 LYS cc_start: 0.7577 (pptt) cc_final: 0.7114 (ptmt) REVERT: K 2142 ASP cc_start: 0.7929 (m-30) cc_final: 0.7645 (m-30) outliers start: 25 outliers final: 9 residues processed: 113 average time/residue: 0.6230 time to fit residues: 76.2470 Evaluate side-chains 97 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 70 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 0.3980 chunk 116 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 117 optimal weight: 0.0970 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** K2339 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 = 0.4625 r_free = 0.4625 target = 0.187992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125631 restraints weight = 20114.568| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.64 r_work: 0.3517 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11553 Z= 0.141 Angle : 0.571 13.271 15565 Z= 0.290 Chirality : 0.039 0.219 1726 Planarity : 0.004 0.044 2019 Dihedral : 3.905 29.294 1489 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.81 % Allowed : 14.79 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.23), residues: 1370 helix: 3.11 (0.16), residues: 941 sheet: -1.91 (0.47), residues: 102 loop : 0.53 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 23 TYR 0.022 0.001 TYR P 77 PHE 0.016 0.002 PHE M 79 TRP 0.007 0.001 TRP N 78 HIS 0.010 0.001 HIS M 74 Details of bonding type rmsd covalent geometry : bond 0.00318 (11553) covalent geometry : angle 0.57076 (15565) hydrogen bonds : bond 0.04259 ( 843) hydrogen bonds : angle 3.81403 ( 2466) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3336 (ppp) cc_final: 0.2186 (tpt) REVERT: M 6 MET cc_start: 0.6885 (mtt) cc_final: 0.6589 (mtt) REVERT: M 25 TYR cc_start: 0.8603 (t80) cc_final: 0.8000 (t80) REVERT: M 104 CYS cc_start: 0.9377 (m) cc_final: 0.8573 (p) REVERT: N 55 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6327 (mmp-170) REVERT: N 170 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7417 (mmm) REVERT: P 119 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6634 (tmmm) REVERT: P 130 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7619 (tp30) REVERT: G 136 ASP cc_start: 0.8143 (t0) cc_final: 0.7787 (m-30) REVERT: K 2142 ASP cc_start: 0.7918 (m-30) cc_final: 0.7641 (m-30) REVERT: Z 214 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5846 (tp40) outliers start: 23 outliers final: 10 residues processed: 100 average time/residue: 0.6181 time to fit residues: 67.0423 Evaluate side-chains 97 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2137 VAL Chi-restraints excluded: chain K residue 2337 ASP Chi-restraints excluded: chain Z residue 214 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 9.9990 chunk 129 optimal weight: 0.0370 chunk 37 optimal weight: 0.5980 chunk 83 optimal weight: 50.0000 chunk 103 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 chunk 121 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** K2339 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 = 0.4633 r_free = 0.4633 target = 0.188759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127203 restraints weight = 20098.479| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.56 r_work: 0.3551 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11553 Z= 0.129 Angle : 0.565 13.366 15565 Z= 0.286 Chirality : 0.038 0.207 1726 Planarity : 0.004 0.044 2019 Dihedral : 3.863 28.622 1489 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.05 % Allowed : 15.26 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.23), residues: 1370 helix: 3.17 (0.16), residues: 941 sheet: -1.81 (0.47), residues: 102 loop : 0.56 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 23 TYR 0.023 0.001 TYR P 77 PHE 0.016 0.001 PHE M 79 TRP 0.006 0.001 TRP N 78 HIS 0.009 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00286 (11553) covalent geometry : angle 0.56475 (15565) hydrogen bonds : bond 0.04066 ( 843) hydrogen bonds : angle 3.74487 ( 2466) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3405 (ppp) cc_final: 0.1688 (tpt) REVERT: M 6 MET cc_start: 0.6780 (mtt) cc_final: 0.6529 (mtt) REVERT: M 25 TYR cc_start: 0.8562 (t80) cc_final: 0.8041 (t80) REVERT: M 92 ARG cc_start: 0.7173 (tpp-160) cc_final: 0.6891 (tpp-160) REVERT: M 104 CYS cc_start: 0.9372 (m) cc_final: 0.8562 (p) REVERT: N 170 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7217 (mmm) REVERT: P 119 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6622 (tmmm) REVERT: P 130 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: G 136 ASP cc_start: 0.8057 (t0) cc_final: 0.7677 (m-30) REVERT: K 2142 ASP cc_start: 0.7918 (m-30) cc_final: 0.7646 (m-30) outliers start: 26 outliers final: 10 residues processed: 110 average time/residue: 0.5320 time to fit residues: 63.6508 Evaluate side-chains 98 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 GLN ** K2339 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 = 0.4615 r_free = 0.4615 target = 0.187102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.124728 restraints weight = 20060.374| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.55 r_work: 0.3511 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11553 Z= 0.166 Angle : 0.600 13.517 15565 Z= 0.304 Chirality : 0.040 0.199 1726 Planarity : 0.004 0.045 2019 Dihedral : 3.989 29.616 1489 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.49 % Allowed : 15.89 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.23), residues: 1370 helix: 3.04 (0.16), residues: 940 sheet: -1.98 (0.47), residues: 102 loop : 0.51 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 23 TYR 0.026 0.002 TYR P 77 PHE 0.016 0.002 PHE G 210 TRP 0.009 0.001 TRP N 78 HIS 0.010 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00387 (11553) covalent geometry : angle 0.60036 (15565) hydrogen bonds : bond 0.04393 ( 843) hydrogen bonds : angle 3.86523 ( 2466) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3233 (ppp) cc_final: 0.1637 (tpt) REVERT: M 6 MET cc_start: 0.6863 (mtt) cc_final: 0.6556 (mtt) REVERT: M 25 TYR cc_start: 0.8575 (t80) cc_final: 0.7976 (t80) REVERT: M 92 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6970 (tpp-160) REVERT: N 170 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7251 (mmm) REVERT: P 119 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6642 (tmmm) REVERT: P 130 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: G 136 ASP cc_start: 0.8056 (t0) cc_final: 0.7718 (m-30) REVERT: K 2142 ASP cc_start: 0.7910 (m-30) cc_final: 0.7622 (m-30) outliers start: 19 outliers final: 10 residues processed: 102 average time/residue: 0.5346 time to fit residues: 59.4452 Evaluate side-chains 100 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 108 optimal weight: 50.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 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 = 0.4607 r_free = 0.4607 target = 0.186246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123354 restraints weight = 20288.334| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.63 r_work: 0.3487 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11553 Z= 0.194 Angle : 0.634 13.554 15565 Z= 0.324 Chirality : 0.041 0.199 1726 Planarity : 0.004 0.045 2019 Dihedral : 4.072 29.353 1489 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.42 % Allowed : 16.21 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.23), residues: 1370 helix: 2.92 (0.16), residues: 934 sheet: -2.01 (0.47), residues: 100 loop : 0.40 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 23 TYR 0.027 0.002 TYR P 77 PHE 0.018 0.002 PHE G 210 TRP 0.010 0.001 TRP K2212 HIS 0.011 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00457 (11553) covalent geometry : angle 0.63406 (15565) hydrogen bonds : bond 0.04585 ( 843) hydrogen bonds : angle 3.96649 ( 2466) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3130 (ppp) cc_final: 0.1472 (tpt) REVERT: M 25 TYR cc_start: 0.8601 (t80) cc_final: 0.8021 (t80) REVERT: M 92 ARG cc_start: 0.7291 (tpp-160) cc_final: 0.6808 (tpp-160) REVERT: N 170 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7370 (mpp) REVERT: P 119 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6605 (tmmm) REVERT: P 130 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: K 2142 ASP cc_start: 0.7910 (m-30) cc_final: 0.7626 (m-30) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 0.5566 time to fit residues: 61.2422 Evaluate side-chains 100 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 126 optimal weight: 0.0670 chunk 94 optimal weight: 50.0000 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 92 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.183850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.121070 restraints weight = 20417.299| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.53 r_work: 0.3559 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11553 Z= 0.128 Angle : 0.582 13.328 15565 Z= 0.297 Chirality : 0.039 0.197 1726 Planarity : 0.004 0.043 2019 Dihedral : 3.930 28.589 1489 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.18 % Allowed : 16.68 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.23 (0.24), residues: 1370 helix: 3.13 (0.16), residues: 940 sheet: -1.84 (0.48), residues: 101 loop : 0.50 (0.40), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 23 TYR 0.026 0.001 TYR P 77 PHE 0.014 0.001 PHE M 79 TRP 0.007 0.001 TRP K2135 HIS 0.011 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00280 (11553) covalent geometry : angle 0.58222 (15565) hydrogen bonds : bond 0.04127 ( 843) hydrogen bonds : angle 3.81570 ( 2466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.45 seconds wall clock time: 81 minutes 45.80 seconds (4905.80 seconds total)