Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:21:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/11_2022/7qwm_14189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/11_2022/7qwm_14189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/11_2022/7qwm_14189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/11_2022/7qwm_14189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/11_2022/7qwm_14189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/11_2022/7qwm_14189.pdb" } resolution = 2.76 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 ------------------------------------------------------------------------------- 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3255 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "B" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "C" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Time building chain proxies: 2.31, per 1000 atoms: 0.71 Number of scatterers: 3255 At special positions: 0 Unit cell: (87.874, 114.402, 36.476, 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 21 16.00 O 636 8.00 N 519 7.00 C 2079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 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: 1.06 Conformation dependent library (CDL) restraints added in 469.8 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 66.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126 removed outlier: 6.170A pdb=" N ILE A 121 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LYS B 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE B 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 121 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LYS C 124 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.812A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 138 removed outlier: 6.415A pdb=" N SER A 134 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL B 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 136 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 153 removed outlier: 7.041A pdb=" N TYR A 143 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 144 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 145 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR B 143 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU C 144 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 145 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.477A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR B 157 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL C 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER B 159 " --> pdb=" O VAL C 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 176 removed outlier: 6.973A pdb=" N SER A 172 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 173 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER B 172 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS C 173 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.438A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.229A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213 removed outlier: 9.091A pdb=" N THR A 201 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N ALA B 204 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A 203 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLU B 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A 205 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER B 208 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET A 207 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET B 210 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N THR B 201 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ALA C 204 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE B 203 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N GLU C 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 205 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N SER C 208 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET B 207 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET C 210 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR B 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP C 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.073A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 219 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER A 218 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 245 removed outlier: 9.072A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 230 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 231 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR B 235 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 236 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE B 237 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY C 238 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS B 239 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER C 240 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 241 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C 242 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 243 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER C 244 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN B 245 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.806A pdb=" N GLN A 249 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASP B 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 56 hydrogen bonds defined for protein. 168 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: 0.72 Time building geometry restraints manager: 1.17 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: 943 1.33 - 1.46: 532 1.46 - 1.58: 1798 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 3309 Sorted by residual: bond pdb=" N ILE C 146 " pdb=" CA ILE C 146 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.14e-02 7.69e+03 7.44e+00 bond pdb=" CZ ARG B 140 " pdb=" NH2 ARG B 140 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.59e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.48e+00 bond pdb=" CZ ARG B 180 " pdb=" NH2 ARG B 180 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.47e+00 bond pdb=" CZ ARG C 140 " pdb=" NH2 ARG C 140 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.44e+00 ... (remaining 3304 not shown) Histogram of bond angle deviations from ideal: 99.17 - 105.01: 49 105.01 - 110.86: 893 110.86 - 116.70: 1277 116.70 - 122.54: 1781 122.54 - 128.39: 497 Bond angle restraints: 4497 Sorted by residual: angle pdb=" N THR C 231 " pdb=" CA THR C 231 " pdb=" C THR C 231 " ideal model delta sigma weight residual 112.45 121.41 -8.96 1.39e+00 5.18e-01 4.16e+01 angle pdb=" CB ASN B 183 " pdb=" CG ASN B 183 " pdb=" ND2 ASN B 183 " ideal model delta sigma weight residual 116.40 107.32 9.08 1.50e+00 4.44e-01 3.66e+01 angle pdb=" N GLN B 138 " pdb=" CA GLN B 138 " pdb=" C GLN B 138 " ideal model delta sigma weight residual 108.60 117.03 -8.43 1.46e+00 4.69e-01 3.33e+01 angle pdb=" CA ASN C 145 " pdb=" CB ASN C 145 " pdb=" CG ASN C 145 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " pdb=" CG ASN B 183 " ideal model delta sigma weight residual 112.60 118.15 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 4492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 1782 14.90 - 29.81: 164 29.81 - 44.71: 28 44.71 - 59.61: 13 59.61 - 74.51: 8 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N MET A 207 " pdb=" CA MET A 207 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU C 206 " pdb=" C GLU C 206 " pdb=" N MET C 207 " pdb=" CA MET C 207 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU B 206 " pdb=" C GLU B 206 " pdb=" N MET B 207 " pdb=" CA MET B 207 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 415 0.112 - 0.224: 104 0.224 - 0.337: 13 0.337 - 0.449: 5 0.449 - 0.561: 3 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA THR A 231 " pdb=" N THR A 231 " pdb=" C THR A 231 " pdb=" CB THR A 231 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA THR C 231 " pdb=" N THR C 231 " pdb=" C THR C 231 " pdb=" CB THR C 231 " both_signs ideal model delta sigma weight residual False 2.53 2.01 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA LYS B 193 " pdb=" N LYS B 193 " pdb=" C LYS B 193 " pdb=" CB LYS B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 537 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 250 " 0.056 2.00e-02 2.50e+03 3.68e-02 2.71e+01 pdb=" CG TYR A 250 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 250 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 250 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 250 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 250 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 250 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 250 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " 0.053 2.00e-02 2.50e+03 3.25e-02 1.85e+01 pdb=" CG PHE A 171 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 248 " -0.054 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR B 248 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 248 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 248 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 248 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 248 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 248 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 248 " -0.044 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1535 2.98 - 3.46: 2771 3.46 - 3.94: 5653 3.94 - 4.42: 5664 4.42 - 4.90: 10689 Nonbonded interactions: 26312 Sorted by model distance: nonbonded pdb=" OG SER A 120 " pdb=" OE2 GLU B 161 " model vdw 2.502 2.440 nonbonded pdb=" OG SER B 120 " pdb=" OE2 GLU C 161 " model vdw 2.570 2.440 nonbonded pdb=" O GLY A 127 " pdb=" OH TYR B 248 " model vdw 2.631 2.440 nonbonded pdb=" O GLY B 127 " pdb=" OH TYR C 248 " model vdw 2.658 2.440 nonbonded pdb=" OE1 GLN B 229 " pdb=" OG SER B 240 " model vdw 2.665 2.440 ... (remaining 26307 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2079 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.150 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: 6.670 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.012 0.038 3309 Z= 0.799 Angle : 1.929 9.079 4497 Z= 1.266 Chirality : 0.107 0.561 540 Planarity : 0.011 0.043 558 Dihedral : 13.263 74.511 1206 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 50.00 % 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: -2.89 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.25), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.0417 time to fit residues: 127.6355 Evaluate side-chains 85 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 151 ASN B 164 ASN B 194 GLN C 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 3309 Z= 0.240 Angle : 0.696 7.116 4497 Z= 0.381 Chirality : 0.055 0.133 540 Planarity : 0.003 0.015 558 Dihedral : 7.233 23.052 447 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.73 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.396 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 97 average time/residue: 1.1297 time to fit residues: 112.5627 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.5433 time to fit residues: 2.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 3309 Z= 0.352 Angle : 0.728 5.524 4497 Z= 0.403 Chirality : 0.056 0.151 540 Planarity : 0.003 0.022 558 Dihedral : 7.212 25.502 447 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.82 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.398 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 95 average time/residue: 1.2324 time to fit residues: 120.0384 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.5120 time to fit residues: 3.6098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 3309 Z= 0.209 Angle : 0.607 6.111 4497 Z= 0.336 Chirality : 0.053 0.138 540 Planarity : 0.003 0.018 558 Dihedral : 6.746 22.762 447 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.85 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.427 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 97 average time/residue: 1.1296 time to fit residues: 112.5856 Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.0370 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3309 Z= 0.276 Angle : 0.658 5.892 4497 Z= 0.368 Chirality : 0.053 0.130 540 Planarity : 0.003 0.020 558 Dihedral : 6.811 23.875 447 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.85 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.423 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 91 average time/residue: 1.2742 time to fit residues: 118.8044 Evaluate side-chains 88 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 3309 Z= 0.276 Angle : 0.649 6.298 4497 Z= 0.360 Chirality : 0.053 0.131 540 Planarity : 0.003 0.018 558 Dihedral : 6.805 24.981 447 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.85 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.450 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 93 average time/residue: 1.2069 time to fit residues: 115.1268 Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3309 Z= 0.161 Angle : 0.553 4.938 4497 Z= 0.310 Chirality : 0.051 0.137 540 Planarity : 0.002 0.020 558 Dihedral : 6.457 23.546 447 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.81 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.326 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 92 average time/residue: 1.2125 time to fit residues: 114.4018 Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 21 optimal weight: 0.0770 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3309 Z= 0.166 Angle : 0.568 6.160 4497 Z= 0.320 Chirality : 0.051 0.124 540 Planarity : 0.003 0.024 558 Dihedral : 6.403 24.308 447 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.74 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.355 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 87 average time/residue: 1.2866 time to fit residues: 114.7487 Evaluate side-chains 83 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3309 Z= 0.179 Angle : 0.591 8.585 4497 Z= 0.327 Chirality : 0.052 0.129 540 Planarity : 0.002 0.021 558 Dihedral : 6.455 24.197 447 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.73 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.401 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 1.2949 time to fit residues: 108.7940 Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 0.0170 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3309 Z= 0.270 Angle : 0.663 9.279 4497 Z= 0.367 Chirality : 0.053 0.128 540 Planarity : 0.003 0.032 558 Dihedral : 6.753 25.203 447 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.78 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.393 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 1.2432 time to fit residues: 109.5719 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132187 restraints weight = 3126.533| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.45 r_work: 0.3772 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 1.27 restraints_weight: 0.2500 r_work: 0.3737 rms_B_bonded: 1.44 restraints_weight: 0.1250 r_work: 0.3712 rms_B_bonded: 1.74 restraints_weight: 0.0625 r_work: 0.3679 rms_B_bonded: 2.24 restraints_weight: 0.0312 r_work: 0.3635 rms_B_bonded: 3.01 restraints_weight: 0.0156 r_work: 0.3574 rms_B_bonded: 4.23 restraints_weight: 0.0078 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3309 Z= 0.261 Angle : 0.660 9.053 4497 Z= 0.365 Chirality : 0.053 0.126 540 Planarity : 0.003 0.030 558 Dihedral : 6.830 25.632 447 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.77 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.27), residues: 399 =============================================================================== Job complete usr+sys time: 2089.10 seconds wall clock time: 38 minutes 19.11 seconds (2299.11 seconds total)