Starting phenix.real_space_refine on Tue Apr 9 15:14:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/04_2024/8wm8_37645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/04_2024/8wm8_37645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/04_2024/8wm8_37645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/04_2024/8wm8_37645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/04_2024/8wm8_37645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/04_2024/8wm8_37645_updated.pdb" } resolution = 3.54 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= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 25 5.16 5 C 5396 2.51 5 N 1374 2.21 5 O 1459 1.98 5 H 8522 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 8": "OD1" <-> "OD2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16776 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4116 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4198 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 17, 'TRANS': 247} Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4170 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 17, 'TRANS': 245} Chain: "C" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4288 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'NO3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.38, per 1000 atoms: 0.50 Number of scatterers: 16776 At special positions: 0 Unit cell: (81.32, 118.77, 95.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 O 1459 8.00 N 1374 7.00 C 5396 6.00 H 8522 1.00 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 - 3.50 Amino acid : False - 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: 12.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 5 sheets defined 47.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 110 through 118 removed outlier: 4.008A pdb=" N ALA D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.710A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.663A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.548A pdb=" N GLU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 220 No H-bonds generated for 'chain 'D' and resid 217 through 220' Processing helix chain 'D' and resid 256 through 270 removed outlier: 4.022A pdb=" N ASP D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE D 270 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.509A pdb=" N PHE B 21 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 56 through 59 No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.539A pdb=" N ILE B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.832A pdb=" N SER B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.823A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.034A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 4.340A pdb=" N VAL B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.664A pdb=" N ILE B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.871A pdb=" N ASN B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 196 through 207 Proline residue: B 201 - end of helix Processing helix chain 'B' and resid 209 through 218 removed outlier: 3.750A pdb=" N LEU B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 245 through 271 removed outlier: 4.031A pdb=" N ILE B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 27 through 45 removed outlier: 3.958A pdb=" N LEU A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.530A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.024A pdb=" N ASN A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.569A pdb=" N THR A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.775A pdb=" N ILE A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.534A pdb=" N ILE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.507A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 123 removed outlier: 3.745A pdb=" N ALA C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.668A pdb=" N VAL C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.825A pdb=" N GLU C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 No H-bonds generated for 'chain 'C' and resid 199 through 202' Processing helix chain 'C' and resid 234 through 237 No H-bonds generated for 'chain 'C' and resid 234 through 237' Processing helix chain 'C' and resid 241 through 268 removed outlier: 3.816A pdb=" N ASN C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 224 through 226 removed outlier: 8.093A pdb=" N VAL D 225 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS D 54 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL D 207 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU D 55 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET D 209 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 208 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 21 through 26 removed outlier: 3.589A pdb=" N LEU D 21 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE D 43 " --> pdb=" O GLY D 25 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.666A pdb=" N LEU D 40 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR D 30 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR D 38 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 38 through 41 Processing sheet with id= E, first strand: chain 'C' and resid 208 through 210 245 hydrogen bonds defined for protein. 678 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: 6.16 Time building geometry restraints manager: 13.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8514 1.03 - 1.23: 9 1.23 - 1.42: 3400 1.42 - 1.62: 4997 1.62 - 1.81: 42 Bond restraints: 16962 Sorted by residual: bond pdb=" N NO3 A 301 " pdb=" O3 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.264 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" N NO3 A 301 " pdb=" O2 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.264 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" N NO3 A 301 " pdb=" O1 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.263 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C ILE B 209 " pdb=" O ILE B 209 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.19e-02 7.06e+03 1.28e+00 bond pdb=" C GLY D 35 " pdb=" N PRO D 36 " ideal model delta sigma weight residual 1.333 1.343 -0.010 1.01e-02 9.80e+03 9.72e-01 ... (remaining 16957 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 428 107.15 - 113.86: 20739 113.86 - 120.58: 5468 120.58 - 127.29: 4135 127.29 - 134.01: 108 Bond angle restraints: 30878 Sorted by residual: angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 113.41 107.47 5.94 1.22e+00 6.72e-01 2.37e+01 angle pdb=" N ASN A 117 " pdb=" CA ASN A 117 " pdb=" C ASN A 117 " ideal model delta sigma weight residual 114.62 109.17 5.45 1.14e+00 7.69e-01 2.28e+01 angle pdb=" N VAL C 106 " pdb=" CA VAL C 106 " pdb=" C VAL C 106 " ideal model delta sigma weight residual 111.62 108.23 3.39 7.90e-01 1.60e+00 1.84e+01 angle pdb=" N ASP D 178 " pdb=" CA ASP D 178 " pdb=" C ASP D 178 " ideal model delta sigma weight residual 110.41 106.28 4.13 1.23e+00 6.61e-01 1.13e+01 angle pdb=" CA ASN A 117 " pdb=" C ASN A 117 " pdb=" N ALA A 118 " ideal model delta sigma weight residual 119.71 116.30 3.41 1.17e+00 7.31e-01 8.47e+00 ... (remaining 30873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7061 17.96 - 35.92: 570 35.92 - 53.88: 221 53.88 - 71.84: 37 71.84 - 89.80: 16 Dihedral angle restraints: 7905 sinusoidal: 4361 harmonic: 3544 Sorted by residual: dihedral pdb=" CA TRP A 235 " pdb=" C TRP A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N ILE A 158 " pdb=" CA ILE A 158 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP A 23 " pdb=" C TRP A 23 " pdb=" N LYS A 24 " pdb=" CA LYS A 24 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 851 0.030 - 0.059: 303 0.059 - 0.089: 118 0.089 - 0.118: 62 0.118 - 0.148: 13 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA ILE B 172 " pdb=" N ILE B 172 " pdb=" C ILE B 172 " pdb=" CB ILE B 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 172 " pdb=" N ILE A 172 " pdb=" C ILE A 172 " pdb=" CB ILE A 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE D 241 " pdb=" N ILE D 241 " pdb=" C ILE D 241 " pdb=" CB ILE D 241 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1344 not shown) Planarity restraints: 2447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 112 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 113 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 146 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 147 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 245 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO D 246 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 246 " 0.022 5.00e-02 4.00e+02 ... (remaining 2444 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 664 2.15 - 2.77: 33045 2.77 - 3.38: 47277 3.38 - 3.99: 59658 3.99 - 4.60: 93421 Nonbonded interactions: 234065 Sorted by model distance: nonbonded pdb=" O ILE A 158 " pdb=" H LEU A 162 " model vdw 1.542 1.850 nonbonded pdb=" O PRO A 160 " pdb="HD21 ASN A 164 " model vdw 1.572 1.850 nonbonded pdb=" OD1 ASP D 267 " pdb="HD21 ASN D 271 " model vdw 1.592 1.850 nonbonded pdb=" O PHE D 219 " pdb="HH11 ARG D 247 " model vdw 1.614 1.850 nonbonded pdb=" OD1 ASN D 263 " pdb=" HH TYR C 244 " model vdw 1.650 1.850 ... (remaining 234060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 277) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 16 through 277)) } 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: 0.010 Normalize map: mean=0, sd=1: 1.400 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: 0.270 Extract box with map and model: 4.570 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 57.090 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.002 0.044 8440 Z= 0.155 Angle : 0.581 5.941 11494 Z= 0.328 Chirality : 0.040 0.148 1347 Planarity : 0.004 0.046 1458 Dihedral : 14.853 89.805 3077 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.26), residues: 1047 helix: -1.14 (0.24), residues: 517 sheet: -2.40 (0.66), residues: 66 loop : -2.07 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.002 0.001 HIS C 240 PHE 0.015 0.001 PHE D 20 TYR 0.011 0.001 TYR D 102 ARG 0.004 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3794 time to fit residues: 99.9238 Evaluate side-chains 150 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.0060 chunk 26 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8440 Z= 0.207 Angle : 0.607 6.279 11494 Z= 0.315 Chirality : 0.042 0.145 1347 Planarity : 0.005 0.045 1458 Dihedral : 5.040 24.839 1122 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.67 % Allowed : 8.58 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.55 (0.25), residues: 1047 helix: -1.12 (0.22), residues: 523 sheet: -2.54 (0.63), residues: 66 loop : -2.16 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.003 0.001 HIS C 219 PHE 0.010 0.001 PHE A 269 TYR 0.017 0.001 TYR A 116 ARG 0.002 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.7903 (t80) cc_final: 0.7658 (t80) REVERT: A 236 ASP cc_start: 0.7785 (t0) cc_final: 0.7490 (t0) outliers start: 6 outliers final: 4 residues processed: 166 average time/residue: 0.3750 time to fit residues: 92.1466 Evaluate side-chains 154 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8440 Z= 0.250 Angle : 0.592 6.962 11494 Z= 0.308 Chirality : 0.042 0.151 1347 Planarity : 0.005 0.045 1458 Dihedral : 5.135 25.302 1122 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.50 % Favored : 91.40 % Rotamer: Outliers : 0.78 % Allowed : 10.93 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.55 (0.25), residues: 1047 helix: -1.10 (0.22), residues: 526 sheet: -2.53 (0.64), residues: 61 loop : -2.20 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS C 43 PHE 0.016 0.001 PHE A 95 TYR 0.013 0.002 TYR B 238 ARG 0.004 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8041 (t80) cc_final: 0.7805 (t80) REVERT: D 204 GLN cc_start: 0.7864 (pm20) cc_final: 0.7523 (pm20) REVERT: A 236 ASP cc_start: 0.7897 (t0) cc_final: 0.7648 (t0) outliers start: 7 outliers final: 5 residues processed: 161 average time/residue: 0.3728 time to fit residues: 87.7856 Evaluate side-chains 157 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8440 Z= 0.175 Angle : 0.561 6.440 11494 Z= 0.288 Chirality : 0.041 0.150 1347 Planarity : 0.004 0.044 1458 Dihedral : 5.035 25.638 1122 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.78 % Allowed : 13.04 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.25), residues: 1047 helix: -0.99 (0.23), residues: 526 sheet: -2.42 (0.65), residues: 60 loop : -2.23 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS D 137 PHE 0.011 0.001 PHE A 95 TYR 0.019 0.001 TYR A 116 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7913 (pm20) cc_final: 0.7628 (pm20) REVERT: A 236 ASP cc_start: 0.7777 (t0) cc_final: 0.7518 (t0) outliers start: 7 outliers final: 5 residues processed: 157 average time/residue: 0.3698 time to fit residues: 86.0273 Evaluate side-chains 152 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN D 137 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8440 Z= 0.236 Angle : 0.576 6.915 11494 Z= 0.297 Chirality : 0.041 0.147 1347 Planarity : 0.005 0.043 1458 Dihedral : 5.089 25.110 1122 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.69 % Favored : 91.21 % Rotamer: Outliers : 0.78 % Allowed : 14.16 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.25), residues: 1047 helix: -0.97 (0.23), residues: 529 sheet: -2.59 (0.63), residues: 61 loop : -2.25 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.004 0.001 HIS D 137 PHE 0.014 0.001 PHE A 95 TYR 0.012 0.001 TYR B 176 ARG 0.004 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7934 (pm20) cc_final: 0.7681 (pm20) REVERT: A 236 ASP cc_start: 0.7888 (t0) cc_final: 0.7642 (t0) outliers start: 7 outliers final: 6 residues processed: 157 average time/residue: 0.3595 time to fit residues: 84.2810 Evaluate side-chains 152 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8440 Z= 0.226 Angle : 0.574 6.861 11494 Z= 0.295 Chirality : 0.041 0.150 1347 Planarity : 0.005 0.054 1458 Dihedral : 5.112 26.035 1122 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.21 % Favored : 91.69 % Rotamer: Outliers : 0.89 % Allowed : 15.27 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.44 (0.25), residues: 1047 helix: -0.98 (0.23), residues: 535 sheet: -2.56 (0.64), residues: 61 loop : -2.20 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS C 197 PHE 0.014 0.001 PHE A 95 TYR 0.011 0.001 TYR B 238 ARG 0.007 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7923 (pm20) cc_final: 0.7669 (pm20) REVERT: A 236 ASP cc_start: 0.7865 (t0) cc_final: 0.7624 (t0) outliers start: 8 outliers final: 7 residues processed: 153 average time/residue: 0.3506 time to fit residues: 79.3535 Evaluate side-chains 155 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 72 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8440 Z= 0.163 Angle : 0.552 6.396 11494 Z= 0.281 Chirality : 0.041 0.150 1347 Planarity : 0.005 0.044 1458 Dihedral : 4.958 24.895 1122 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.16 % Favored : 92.74 % Rotamer: Outliers : 0.78 % Allowed : 15.27 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.24 (0.26), residues: 1047 helix: -0.80 (0.23), residues: 526 sheet: -2.45 (0.65), residues: 61 loop : -2.10 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.003 0.001 HIS C 122 PHE 0.009 0.001 PHE D 20 TYR 0.014 0.001 TYR D 102 ARG 0.006 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7956 (pm20) cc_final: 0.7705 (pm20) REVERT: A 144 GLN cc_start: 0.8044 (mp10) cc_final: 0.7839 (mp10) REVERT: A 236 ASP cc_start: 0.7833 (t0) cc_final: 0.7588 (t0) outliers start: 7 outliers final: 7 residues processed: 157 average time/residue: 0.3517 time to fit residues: 82.0253 Evaluate side-chains 155 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8440 Z= 0.186 Angle : 0.557 6.475 11494 Z= 0.285 Chirality : 0.041 0.149 1347 Planarity : 0.005 0.044 1458 Dihedral : 4.956 24.984 1122 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 0.78 % Allowed : 15.94 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.20 (0.26), residues: 1047 helix: -0.78 (0.23), residues: 533 sheet: -2.43 (0.66), residues: 61 loop : -2.08 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.004 0.001 HIS C 197 PHE 0.010 0.001 PHE A 95 TYR 0.011 0.001 TYR D 102 ARG 0.005 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7999 (pm20) cc_final: 0.7730 (pm20) REVERT: A 144 GLN cc_start: 0.8130 (mp10) cc_final: 0.7914 (mp10) REVERT: A 236 ASP cc_start: 0.7833 (t0) cc_final: 0.7592 (t0) outliers start: 7 outliers final: 7 residues processed: 153 average time/residue: 0.3497 time to fit residues: 79.3352 Evaluate side-chains 156 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8440 Z= 0.272 Angle : 0.593 7.091 11494 Z= 0.306 Chirality : 0.042 0.145 1347 Planarity : 0.005 0.043 1458 Dihedral : 5.127 25.541 1122 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.17 % Favored : 90.74 % Rotamer: Outliers : 0.89 % Allowed : 16.83 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.26), residues: 1047 helix: -0.87 (0.23), residues: 533 sheet: -2.54 (0.66), residues: 61 loop : -2.13 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.003 0.001 HIS C 197 PHE 0.017 0.001 PHE A 95 TYR 0.016 0.002 TYR B 176 ARG 0.005 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7913 (pm20) cc_final: 0.7644 (pm20) REVERT: A 144 GLN cc_start: 0.8243 (mp10) cc_final: 0.8009 (mp10) REVERT: A 236 ASP cc_start: 0.7893 (t0) cc_final: 0.7661 (t0) outliers start: 8 outliers final: 7 residues processed: 152 average time/residue: 0.3448 time to fit residues: 78.2425 Evaluate side-chains 155 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.0050 chunk 87 optimal weight: 0.0170 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8440 Z= 0.169 Angle : 0.568 7.085 11494 Z= 0.289 Chirality : 0.041 0.154 1347 Planarity : 0.005 0.044 1458 Dihedral : 4.996 25.556 1122 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.16 % Favored : 92.74 % Rotamer: Outliers : 1.00 % Allowed : 17.17 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.14 (0.26), residues: 1047 helix: -0.71 (0.23), residues: 533 sheet: -2.37 (0.67), residues: 61 loop : -2.09 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS D 137 PHE 0.015 0.001 PHE D 20 TYR 0.014 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 204 GLN cc_start: 0.7982 (pm20) cc_final: 0.7644 (pm20) REVERT: A 144 GLN cc_start: 0.8231 (mp10) cc_final: 0.7998 (mp10) REVERT: A 236 ASP cc_start: 0.7839 (t0) cc_final: 0.7593 (t0) outliers start: 9 outliers final: 8 residues processed: 151 average time/residue: 0.3448 time to fit residues: 77.5710 Evaluate side-chains 154 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.149425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116596 restraints weight = 34559.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122427 restraints weight = 15940.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126123 restraints weight = 9875.530| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8440 Z= 0.171 Angle : 0.558 7.067 11494 Z= 0.284 Chirality : 0.041 0.148 1347 Planarity : 0.005 0.045 1458 Dihedral : 4.927 24.513 1122 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 0.89 % Allowed : 17.28 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.05 (0.26), residues: 1047 helix: -0.62 (0.24), residues: 533 sheet: -2.29 (0.68), residues: 61 loop : -2.08 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.004 0.001 HIS D 137 PHE 0.015 0.001 PHE D 20 TYR 0.012 0.001 TYR D 102 ARG 0.006 0.000 ARG C 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3884.15 seconds wall clock time: 69 minutes 49.85 seconds (4189.85 seconds total)