Starting phenix.real_space_refine on Sun Mar 10 16:09:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/03_2024/7qwm_14189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/03_2024/7qwm_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_14189/03_2024/7qwm_14189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/03_2024/7qwm_14189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/03_2024/7qwm_14189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwm_14189/03_2024/7qwm_14189.pdb" } resolution = 2.76 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= 0.000 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 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. 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-5265/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: 2.34, per 1000 atoms: 0.72 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: 1.16 Conformation dependent library (CDL) restraints added in 584.2 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: 0.42 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: 0.80 Time building geometry restraints manager: 1.28 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 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: 1.360 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: 0.000 Extract box with map and model: 6.700 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 239 PHE 0.053 0.012 PHE A 171 TYR 0.066 0.015 TYR A 250 ARG 0.007 0.002 ARG C 247 *********************** 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 : 0.408 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7553 (mttt) cc_final: 0.7236 (mttm) REVERT: A 145 ASN cc_start: 0.7161 (m-40) cc_final: 0.6885 (m-40) REVERT: B 140 ARG cc_start: 0.6423 (mtt-85) cc_final: 0.6198 (mmm-85) REVERT: B 173 LYS cc_start: 0.7358 (tttt) cc_final: 0.7007 (tttt) REVERT: B 196 ASP cc_start: 0.7314 (t0) cc_final: 0.6969 (t0) REVERT: B 202 VAL cc_start: 0.8110 (t) cc_final: 0.7900 (t) REVERT: B 205 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5932 (mt-10) REVERT: C 140 ARG cc_start: 0.6769 (mtt-85) cc_final: 0.6345 (mmm-85) REVERT: C 159 SER cc_start: 0.8232 (t) cc_final: 0.8013 (m) REVERT: C 173 LYS cc_start: 0.7555 (tttt) cc_final: 0.7220 (tttt) REVERT: C 196 ASP cc_start: 0.7459 (t0) cc_final: 0.7004 (t0) REVERT: C 205 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6126 (mt-10) REVERT: C 210 MET cc_start: 0.7267 (mtt) cc_final: 0.7044 (mtp) REVERT: C 246 GLU cc_start: 0.7185 (mt-10) cc_final: 0.5886 (mp0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.1073 time to fit residues: 135.5024 Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 164 ASN B 194 GLN C 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3309 Z= 0.236 Angle : 0.709 8.532 4497 Z= 0.388 Chirality : 0.055 0.132 540 Planarity : 0.003 0.016 558 Dihedral : 7.231 22.991 447 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.85 % Allowed : 11.11 % Favored : 87.04 % 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: -2.72 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 239 PHE 0.014 0.003 PHE B 213 TYR 0.018 0.002 TYR A 248 ARG 0.002 0.001 ARG A 247 *********************** 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 100 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8311 (mp) cc_final: 0.7987 (mt) REVERT: A 171 PHE cc_start: 0.7711 (m-80) cc_final: 0.7478 (m-80) REVERT: A 178 LYS cc_start: 0.6552 (tttt) cc_final: 0.6233 (mttp) REVERT: A 180 ARG cc_start: 0.6259 (ttm-80) cc_final: 0.5696 (mmt-90) REVERT: A 205 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6210 (mt-10) REVERT: B 140 ARG cc_start: 0.6435 (mtt-85) cc_final: 0.6170 (mmm-85) REVERT: B 161 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 205 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6035 (mm-30) REVERT: B 207 MET cc_start: 0.6161 (mmt) cc_final: 0.5440 (mmm) REVERT: C 140 ARG cc_start: 0.6778 (mtt-85) cc_final: 0.6372 (mmm-85) REVERT: C 145 ASN cc_start: 0.6885 (m-40) cc_final: 0.6608 (m110) REVERT: C 162 VAL cc_start: 0.8164 (t) cc_final: 0.7674 (m) REVERT: C 191 ASP cc_start: 0.7733 (t0) cc_final: 0.7527 (t70) REVERT: C 196 ASP cc_start: 0.7145 (t0) cc_final: 0.6832 (t0) REVERT: C 205 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6190 (mt-10) REVERT: C 246 GLU cc_start: 0.7274 (mt-10) cc_final: 0.5958 (mp0) outliers start: 7 outliers final: 1 residues processed: 96 average time/residue: 1.2523 time to fit residues: 123.3232 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 3309 Z= 0.377 Angle : 0.749 7.908 4497 Z= 0.414 Chirality : 0.057 0.163 540 Planarity : 0.004 0.024 558 Dihedral : 7.291 25.527 447 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.44 % Allowed : 12.70 % Favored : 83.86 % 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: -2.83 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 239 PHE 0.017 0.003 PHE A 237 TYR 0.017 0.003 TYR B 143 ARG 0.004 0.001 ARG B 180 *********************** 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 105 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7944 (t) cc_final: 0.7429 (m) REVERT: A 178 LYS cc_start: 0.6592 (tttt) cc_final: 0.6221 (mttp) REVERT: A 180 ARG cc_start: 0.6326 (ttm-80) cc_final: 0.5712 (mmt-90) REVERT: A 205 GLU cc_start: 0.6817 (mt-10) cc_final: 0.5932 (tt0) REVERT: B 140 ARG cc_start: 0.6501 (mtt-85) cc_final: 0.6221 (mmm-85) REVERT: B 161 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7345 (mt-10) REVERT: B 205 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6107 (mm-30) REVERT: B 207 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5595 (mmm) REVERT: C 140 ARG cc_start: 0.6929 (mtt-85) cc_final: 0.6531 (mmm-85) REVERT: C 173 LYS cc_start: 0.7611 (tttt) cc_final: 0.7158 (tttt) REVERT: C 205 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6353 (mt-10) outliers start: 13 outliers final: 4 residues processed: 99 average time/residue: 1.3356 time to fit residues: 135.3680 Evaluate side-chains 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3309 Z= 0.277 Angle : 0.661 6.864 4497 Z= 0.365 Chirality : 0.054 0.137 540 Planarity : 0.003 0.021 558 Dihedral : 7.011 24.357 447 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.17 % Allowed : 15.87 % Favored : 80.95 % 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: -2.90 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.013 0.003 PHE A 237 TYR 0.015 0.002 TYR A 248 ARG 0.005 0.001 ARG B 180 *********************** 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 102 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7678 (mttp) cc_final: 0.7461 (mppt) REVERT: A 162 VAL cc_start: 0.7865 (t) cc_final: 0.7379 (m) REVERT: A 180 ARG cc_start: 0.6339 (ttm-80) cc_final: 0.5706 (mmt-90) REVERT: A 193 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7604 (mtpp) REVERT: A 205 GLU cc_start: 0.6854 (mt-10) cc_final: 0.5994 (tt0) REVERT: B 140 ARG cc_start: 0.6514 (mtt-85) cc_final: 0.6232 (mmm-85) REVERT: B 205 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6064 (mm-30) REVERT: B 207 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5506 (mmm) REVERT: C 140 ARG cc_start: 0.6938 (mtt-85) cc_final: 0.6548 (mmm-85) REVERT: C 161 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7149 (mt-10) REVERT: C 162 VAL cc_start: 0.8211 (t) cc_final: 0.7654 (m) REVERT: C 173 LYS cc_start: 0.7607 (tttt) cc_final: 0.7183 (tttt) REVERT: C 205 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6374 (mt-10) REVERT: C 246 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6054 (mp0) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 1.2913 time to fit residues: 128.2592 Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.7732 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3309 Z= 0.310 Angle : 0.673 6.336 4497 Z= 0.374 Chirality : 0.054 0.134 540 Planarity : 0.003 0.023 558 Dihedral : 7.041 24.465 447 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.23 % Allowed : 15.08 % Favored : 80.69 % 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: -2.93 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.014 0.003 PHE A 237 TYR 0.015 0.002 TYR B 143 ARG 0.005 0.001 ARG B 180 *********************** 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 106 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7670 (mttp) cc_final: 0.7456 (mppt) REVERT: A 162 VAL cc_start: 0.7894 (t) cc_final: 0.7392 (m) REVERT: A 163 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6522 (mm-30) REVERT: A 180 ARG cc_start: 0.6436 (ttm-80) cc_final: 0.5687 (mmt-90) REVERT: A 193 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7713 (mtpp) REVERT: A 205 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6051 (tt0) REVERT: B 140 ARG cc_start: 0.6552 (mtt-85) cc_final: 0.6269 (mmm-85) REVERT: B 162 VAL cc_start: 0.7855 (t) cc_final: 0.7314 (m) REVERT: B 205 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6086 (mm-30) REVERT: B 207 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5516 (mmm) REVERT: C 140 ARG cc_start: 0.6961 (mtt-85) cc_final: 0.6577 (mmm-85) REVERT: C 161 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7128 (mt-10) REVERT: C 162 VAL cc_start: 0.8094 (t) cc_final: 0.7479 (m) REVERT: C 173 LYS cc_start: 0.7636 (tttt) cc_final: 0.7231 (tttt) REVERT: C 205 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6478 (mt-10) REVERT: C 246 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6046 (mp0) outliers start: 16 outliers final: 6 residues processed: 96 average time/residue: 1.3319 time to fit residues: 130.8596 Evaluate side-chains 99 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 30.0000 chunk 37 optimal weight: 0.0070 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.3204 ------------------------------------------------------------------------------- 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: 0.7730 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3309 Z= 0.276 Angle : 0.642 5.797 4497 Z= 0.357 Chirality : 0.053 0.134 540 Planarity : 0.003 0.020 558 Dihedral : 6.956 25.246 447 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.17 % Allowed : 17.99 % Favored : 78.84 % 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: -2.95 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.013 0.003 PHE A 237 TYR 0.014 0.002 TYR B 248 ARG 0.005 0.001 ARG B 180 *********************** 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 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7880 (t) cc_final: 0.7386 (m) REVERT: A 163 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6447 (mm-30) REVERT: A 180 ARG cc_start: 0.6473 (ttm-80) cc_final: 0.5718 (mmt-90) REVERT: A 193 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7667 (mtpp) REVERT: A 205 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6127 (tt0) REVERT: B 140 ARG cc_start: 0.6443 (mtt-85) cc_final: 0.6142 (mmm-85) REVERT: B 162 VAL cc_start: 0.7874 (t) cc_final: 0.7345 (m) REVERT: B 207 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5542 (mmm) REVERT: C 140 ARG cc_start: 0.6902 (mtt-85) cc_final: 0.6519 (mmm-85) REVERT: C 161 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7179 (mt-10) REVERT: C 162 VAL cc_start: 0.8093 (t) cc_final: 0.7487 (m) REVERT: C 173 LYS cc_start: 0.7646 (tttt) cc_final: 0.7444 (tttp) REVERT: C 205 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6398 (mt-10) REVERT: C 246 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6028 (mp0) outliers start: 12 outliers final: 4 residues processed: 96 average time/residue: 1.3677 time to fit residues: 134.2730 Evaluate side-chains 98 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.7734 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 3309 Z= 0.289 Angle : 0.650 5.594 4497 Z= 0.363 Chirality : 0.054 0.134 540 Planarity : 0.003 0.020 558 Dihedral : 6.962 25.179 447 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.38 % Allowed : 19.84 % Favored : 77.78 % 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: -2.95 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.014 0.003 PHE A 237 TYR 0.014 0.002 TYR B 248 ARG 0.006 0.001 ARG B 180 *********************** 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 98 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7889 (t) cc_final: 0.7393 (m) REVERT: A 163 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6469 (mm-30) REVERT: A 180 ARG cc_start: 0.6476 (ttm-80) cc_final: 0.5736 (mmt-90) REVERT: A 193 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7725 (mtpp) REVERT: A 205 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6111 (tt0) REVERT: B 140 ARG cc_start: 0.6437 (mtt-85) cc_final: 0.6157 (mmm-85) REVERT: B 162 VAL cc_start: 0.7829 (t) cc_final: 0.7302 (m) REVERT: B 163 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6773 (mt-10) REVERT: B 207 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5513 (mmm) REVERT: C 140 ARG cc_start: 0.6904 (mtt-85) cc_final: 0.6566 (mmm-85) REVERT: C 161 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7200 (mt-10) REVERT: C 162 VAL cc_start: 0.8093 (t) cc_final: 0.7485 (m) REVERT: C 205 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6477 (mt-10) REVERT: C 246 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6047 (mp0) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 1.4034 time to fit residues: 133.4568 Evaluate side-chains 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 27 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.6742 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3309 Z= 0.181 Angle : 0.574 4.964 4497 Z= 0.320 Chirality : 0.052 0.137 540 Planarity : 0.002 0.020 558 Dihedral : 6.657 24.732 447 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.38 % Allowed : 20.37 % Favored : 77.25 % 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: -2.90 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.011 0.002 PHE A 237 TYR 0.012 0.001 TYR B 248 ARG 0.006 0.001 ARG B 180 *********************** 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 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7866 (t) cc_final: 0.7391 (m) REVERT: A 180 ARG cc_start: 0.6438 (ttm-80) cc_final: 0.5787 (mmt-90) REVERT: A 193 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7699 (mtpp) REVERT: A 205 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6198 (tt0) REVERT: B 140 ARG cc_start: 0.6468 (mtt-85) cc_final: 0.6186 (mmm-85) REVERT: B 162 VAL cc_start: 0.7839 (t) cc_final: 0.7337 (m) REVERT: B 207 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5506 (mmm) REVERT: C 140 ARG cc_start: 0.6827 (mtt-85) cc_final: 0.6528 (mmm-85) REVERT: C 161 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7200 (mt-10) REVERT: C 162 VAL cc_start: 0.8073 (t) cc_final: 0.7473 (m) REVERT: C 205 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6545 (mt-10) REVERT: C 246 GLU cc_start: 0.7260 (mt-10) cc_final: 0.5886 (mp0) outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 1.2880 time to fit residues: 121.4961 Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2889 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= 0.167 Angle : 0.577 5.011 4497 Z= 0.326 Chirality : 0.052 0.128 540 Planarity : 0.003 0.030 558 Dihedral : 6.538 25.046 447 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.32 % Allowed : 21.43 % Favored : 77.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.010 0.002 PHE A 237 TYR 0.015 0.001 TYR C 197 ARG 0.006 0.001 ARG B 180 *********************** 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 92 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7858 (t) cc_final: 0.7387 (m) REVERT: A 180 ARG cc_start: 0.6444 (ttm-80) cc_final: 0.5781 (mmt-90) REVERT: A 193 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7584 (mtpp) REVERT: A 205 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6213 (tt0) REVERT: B 140 ARG cc_start: 0.6467 (mtt-85) cc_final: 0.6166 (mmm-85) REVERT: B 162 VAL cc_start: 0.7807 (t) cc_final: 0.7308 (m) REVERT: B 168 GLN cc_start: 0.7639 (mt0) cc_final: 0.7382 (mt0) REVERT: B 171 PHE cc_start: 0.7788 (m-80) cc_final: 0.7507 (m-80) REVERT: B 207 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5510 (mmm) REVERT: B 210 MET cc_start: 0.7217 (mtp) cc_final: 0.6736 (mtp) REVERT: C 140 ARG cc_start: 0.6758 (mtt-85) cc_final: 0.6453 (mmm-85) REVERT: C 161 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7200 (mt-10) REVERT: C 162 VAL cc_start: 0.8060 (t) cc_final: 0.7440 (m) REVERT: C 168 GLN cc_start: 0.7560 (mt0) cc_final: 0.7260 (mt0) REVERT: C 205 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6569 (mt-10) REVERT: C 246 GLU cc_start: 0.7142 (mt-10) cc_final: 0.5729 (mp0) outliers start: 5 outliers final: 1 residues processed: 90 average time/residue: 1.3391 time to fit residues: 123.3250 Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3309 Z= 0.228 Angle : 0.624 7.141 4497 Z= 0.346 Chirality : 0.052 0.131 540 Planarity : 0.002 0.021 558 Dihedral : 6.759 25.829 447 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.32 % Allowed : 21.96 % Favored : 76.72 % 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: -2.90 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.013 0.002 PHE A 237 TYR 0.014 0.002 TYR A 248 ARG 0.006 0.001 ARG B 180 ********************** 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 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7847 (t) cc_final: 0.7337 (m) REVERT: A 163 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6431 (mm-30) REVERT: A 180 ARG cc_start: 0.6478 (ttm-80) cc_final: 0.5793 (mmt-90) REVERT: A 193 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7642 (mtpp) REVERT: A 205 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6135 (tt0) REVERT: B 140 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.6220 (mmm-85) REVERT: B 162 VAL cc_start: 0.7766 (t) cc_final: 0.7256 (m) REVERT: B 168 GLN cc_start: 0.7662 (mt0) cc_final: 0.7398 (mt0) REVERT: B 171 PHE cc_start: 0.7826 (m-80) cc_final: 0.7533 (m-80) REVERT: B 207 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5517 (mmm) REVERT: B 210 MET cc_start: 0.7344 (mtp) cc_final: 0.6766 (mtp) REVERT: C 140 ARG cc_start: 0.6847 (mtt-85) cc_final: 0.6524 (mmm-85) REVERT: C 145 ASN cc_start: 0.7166 (m110) cc_final: 0.6704 (m-40) REVERT: C 161 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7189 (mt-10) REVERT: C 162 VAL cc_start: 0.8092 (t) cc_final: 0.7479 (m) REVERT: C 168 GLN cc_start: 0.7569 (mt0) cc_final: 0.7259 (mt0) REVERT: C 205 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6536 (mt-10) REVERT: C 246 GLU cc_start: 0.7205 (mt-10) cc_final: 0.5794 (mp0) outliers start: 5 outliers final: 1 residues processed: 90 average time/residue: 1.3723 time to fit residues: 126.3294 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.150528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129824 restraints weight = 3175.912| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.46 r_work: 0.3683 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2846 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= 0.220 Angle : 0.641 11.863 4497 Z= 0.349 Chirality : 0.053 0.128 540 Planarity : 0.002 0.022 558 Dihedral : 6.797 26.065 447 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.32 % Allowed : 22.22 % Favored : 76.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.012 0.002 PHE A 237 TYR 0.014 0.002 TYR A 248 ARG 0.006 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.57 seconds wall clock time: 42 minutes 14.47 seconds (2534.47 seconds total)