Starting phenix.real_space_refine on Fri Jul 19 21:38:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/07_2024/8kfy_37208.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/07_2024/8kfy_37208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/07_2024/8kfy_37208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/07_2024/8kfy_37208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/07_2024/8kfy_37208.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/07_2024/8kfy_37208.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 66 5.16 5 C 5754 2.51 5 N 1505 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'OXF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.60 Number of scatterers: 8992 At special positions: 0 Unit cell: (94.64, 120.64, 128.96, 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 66 16.00 O 1667 8.00 N 1505 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 39.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.137A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.524A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.145A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.790A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.702A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.600A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.621A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 31 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.831A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 191 through 205 removed outlier: 3.799A pdb=" N LYS R 195 " --> pdb=" O THR R 191 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN R 199 " --> pdb=" O LYS R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.637A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 266 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.887A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 4.003A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.266A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.813A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.093A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.194A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.810A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.534A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.405A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.616A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.528A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2856 1.34 - 1.46: 2115 1.46 - 1.58: 4116 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9182 Sorted by residual: bond pdb=" CA TYR S 161 " pdb=" CB TYR S 161 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.47e-02 4.63e+03 3.61e+00 bond pdb=" C12 OXF R 601 " pdb=" O3 OXF R 601 " ideal model delta sigma weight residual 1.363 1.391 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" SD MET R 105 " pdb=" CE MET R 105 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.72e+00 bond pdb=" C MET R 105 " pdb=" O MET R 105 " ideal model delta sigma weight residual 1.237 1.224 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" CG LEU R 278 " pdb=" CD2 LEU R 278 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.34: 105 105.34 - 112.55: 4828 112.55 - 119.75: 2957 119.75 - 126.96: 4439 126.96 - 134.16: 96 Bond angle restraints: 12425 Sorted by residual: angle pdb=" CB MET R 105 " pdb=" CG MET R 105 " pdb=" SD MET R 105 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 angle pdb=" N THR S 198 " pdb=" CA THR S 198 " pdb=" C THR S 198 " ideal model delta sigma weight residual 113.43 109.56 3.87 1.26e+00 6.30e-01 9.45e+00 angle pdb=" CG ARG B 19 " pdb=" CD ARG B 19 " pdb=" NE ARG B 19 " ideal model delta sigma weight residual 112.00 118.59 -6.59 2.20e+00 2.07e-01 8.98e+00 angle pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta sigma weight residual 121.18 115.92 5.26 1.98e+00 2.55e-01 7.05e+00 ... (remaining 12420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4723 17.68 - 35.37: 561 35.37 - 53.05: 143 53.05 - 70.73: 16 70.73 - 88.42: 4 Dihedral angle restraints: 5447 sinusoidal: 2133 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN S 130 " pdb=" C GLN S 130 " pdb=" N ALA S 131 " pdb=" CA ALA S 131 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 969 0.036 - 0.071: 318 0.071 - 0.107: 102 0.107 - 0.142: 20 0.142 - 0.178: 5 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA PHE R 290 " pdb=" N PHE R 290 " pdb=" C PHE R 290 " pdb=" CB PHE R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL R 109 " pdb=" CA VAL R 109 " pdb=" CG1 VAL R 109 " pdb=" CG2 VAL R 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR R 291 " pdb=" CA THR R 291 " pdb=" OG1 THR R 291 " pdb=" CG2 THR R 291 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1411 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 236 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO S 224 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 105 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C MET R 105 " -0.035 2.00e-02 2.50e+03 pdb=" O MET R 105 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS R 106 " 0.012 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 251 2.70 - 3.25: 8859 3.25 - 3.80: 14802 3.80 - 4.35: 19109 4.35 - 4.90: 32205 Nonbonded interactions: 75226 Sorted by model distance: nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.155 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.187 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.249 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 2.440 ... (remaining 75221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9182 Z= 0.226 Angle : 0.537 10.063 12425 Z= 0.300 Chirality : 0.041 0.178 1414 Planarity : 0.004 0.058 1556 Dihedral : 15.791 88.418 3300 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.20 % Allowed : 25.61 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1125 helix: 2.52 (0.26), residues: 398 sheet: 0.62 (0.30), residues: 288 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.003 0.001 HIS R 292 PHE 0.021 0.001 PHE R 84 TYR 0.014 0.001 TYR B 85 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7448 (mpp) cc_final: 0.7088 (mmm) REVERT: A 349 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7578 (mtmm) REVERT: B 19 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: R 46 PHE cc_start: 0.8327 (t80) cc_final: 0.8052 (t80) REVERT: R 202 MET cc_start: 0.7523 (mmm) cc_final: 0.7200 (mtp) REVERT: S 154 LEU cc_start: 0.8196 (tp) cc_final: 0.7943 (tp) outliers start: 2 outliers final: 1 residues processed: 227 average time/residue: 0.2680 time to fit residues: 78.7057 Evaluate side-chains 223 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9182 Z= 0.258 Angle : 0.519 8.235 12425 Z= 0.285 Chirality : 0.042 0.186 1414 Planarity : 0.004 0.057 1556 Dihedral : 4.775 50.654 1252 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.45 % Allowed : 21.56 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1125 helix: 2.56 (0.25), residues: 405 sheet: 0.58 (0.30), residues: 287 loop : -0.41 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.006 0.001 HIS S 155 PHE 0.022 0.001 PHE R 214 TYR 0.015 0.002 TYR S 178 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7379 (mpp) cc_final: 0.7135 (mmm) REVERT: A 266 LEU cc_start: 0.8585 (tp) cc_final: 0.8350 (tt) REVERT: A 279 LYS cc_start: 0.8438 (mttt) cc_final: 0.8236 (mptt) REVERT: A 298 GLU cc_start: 0.6712 (tp30) cc_final: 0.6339 (tp30) REVERT: B 19 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.7023 (mtm-85) REVERT: B 197 ARG cc_start: 0.7000 (mpt-90) cc_final: 0.6633 (mpt-90) REVERT: B 263 THR cc_start: 0.8212 (p) cc_final: 0.7888 (m) REVERT: B 301 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: B 335 PHE cc_start: 0.8523 (m-80) cc_final: 0.8042 (m-80) REVERT: R 46 PHE cc_start: 0.8365 (t80) cc_final: 0.8131 (t80) REVERT: R 124 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8182 (mm) REVERT: R 202 MET cc_start: 0.7624 (mmm) cc_final: 0.7353 (mtp) REVERT: R 215 MET cc_start: 0.8065 (mmm) cc_final: 0.7607 (mpp) REVERT: R 250 PHE cc_start: 0.7180 (m-10) cc_final: 0.6926 (m-10) REVERT: R 257 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8178 (p) REVERT: S 154 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7837 (tp) REVERT: S 160 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8445 (m) outliers start: 44 outliers final: 27 residues processed: 236 average time/residue: 0.2334 time to fit residues: 73.3591 Evaluate side-chains 247 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 83 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.0570 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9182 Z= 0.145 Angle : 0.462 7.473 12425 Z= 0.252 Chirality : 0.040 0.189 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.616 52.660 1252 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.95 % Allowed : 22.87 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1125 helix: 2.69 (0.25), residues: 406 sheet: 0.64 (0.30), residues: 285 loop : -0.37 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 PHE 0.016 0.001 PHE R 214 TYR 0.023 0.001 TYR S 223 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7334 (mpp) cc_final: 0.7015 (mmm) REVERT: A 279 LYS cc_start: 0.8391 (mttt) cc_final: 0.8188 (mptt) REVERT: A 298 GLU cc_start: 0.6775 (tp30) cc_final: 0.6433 (tp30) REVERT: A 345 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7870 (mptt) REVERT: B 19 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.7002 (mtm-85) REVERT: B 134 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7583 (ttp80) REVERT: B 197 ARG cc_start: 0.6960 (mpt-90) cc_final: 0.6597 (mpt-90) REVERT: B 301 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7950 (mtpp) REVERT: B 335 PHE cc_start: 0.8449 (m-80) cc_final: 0.8001 (m-80) REVERT: R 46 PHE cc_start: 0.8384 (t80) cc_final: 0.8135 (t80) REVERT: R 72 VAL cc_start: 0.8090 (t) cc_final: 0.7886 (p) REVERT: R 202 MET cc_start: 0.7590 (mmm) cc_final: 0.7367 (mtp) REVERT: R 250 PHE cc_start: 0.7102 (m-10) cc_final: 0.6870 (m-10) REVERT: R 257 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8153 (p) REVERT: R 278 LEU cc_start: 0.8042 (mm) cc_final: 0.7812 (mt) REVERT: S 34 MET cc_start: 0.8336 (mmm) cc_final: 0.8087 (mmm) REVERT: S 148 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6845 (ttm170) REVERT: S 154 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7859 (tp) REVERT: S 160 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8446 (m) outliers start: 39 outliers final: 25 residues processed: 233 average time/residue: 0.2307 time to fit residues: 71.6215 Evaluate side-chains 244 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9182 Z= 0.278 Angle : 0.506 6.842 12425 Z= 0.276 Chirality : 0.042 0.204 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.705 51.640 1252 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.66 % Allowed : 22.57 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1125 helix: 2.57 (0.25), residues: 407 sheet: 0.52 (0.30), residues: 281 loop : -0.41 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.002 PHE R 214 TYR 0.022 0.002 TYR S 223 ARG 0.003 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7410 (mpp) cc_final: 0.7083 (mmm) REVERT: A 298 GLU cc_start: 0.6741 (tp30) cc_final: 0.6399 (tp30) REVERT: A 349 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7618 (mtmm) REVERT: B 19 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6980 (mtm-85) REVERT: B 134 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7566 (ttp80) REVERT: B 178 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 197 ARG cc_start: 0.7012 (mpt-90) cc_final: 0.6598 (mpt-90) REVERT: B 263 THR cc_start: 0.8248 (p) cc_final: 0.7919 (m) REVERT: B 301 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7977 (mtpp) REVERT: B 335 PHE cc_start: 0.8491 (m-80) cc_final: 0.8062 (m-80) REVERT: R 46 PHE cc_start: 0.8423 (t80) cc_final: 0.8166 (t80) REVERT: R 124 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8256 (mm) REVERT: R 250 PHE cc_start: 0.7075 (m-10) cc_final: 0.6840 (m-10) REVERT: R 257 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (p) REVERT: R 278 LEU cc_start: 0.8214 (mm) cc_final: 0.7955 (mt) REVERT: S 148 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6860 (ttm170) REVERT: S 154 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7869 (tp) REVERT: S 160 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8536 (m) REVERT: S 185 SER cc_start: 0.8389 (m) cc_final: 0.8113 (p) outliers start: 46 outliers final: 32 residues processed: 239 average time/residue: 0.2352 time to fit residues: 74.4708 Evaluate side-chains 251 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 214 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 333 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9182 Z= 0.264 Angle : 0.502 6.815 12425 Z= 0.273 Chirality : 0.041 0.194 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.712 52.324 1252 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.55 % Allowed : 22.27 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1125 helix: 2.49 (0.25), residues: 407 sheet: 0.44 (0.30), residues: 280 loop : -0.45 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.003 0.001 HIS B 91 PHE 0.023 0.001 PHE R 214 TYR 0.022 0.002 TYR S 223 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7474 (mpp) cc_final: 0.7179 (mmm) REVERT: A 298 GLU cc_start: 0.6778 (tp30) cc_final: 0.6418 (tp30) REVERT: A 317 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8034 (ptpp) REVERT: B 19 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6971 (mtm-85) REVERT: B 134 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7562 (ttp80) REVERT: B 197 ARG cc_start: 0.7009 (mpt-90) cc_final: 0.6572 (mpt-90) REVERT: B 251 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8342 (mtt90) REVERT: B 263 THR cc_start: 0.8268 (p) cc_final: 0.7796 (m) REVERT: B 301 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7992 (mtpp) REVERT: B 335 PHE cc_start: 0.8493 (m-80) cc_final: 0.8099 (m-80) REVERT: R 46 PHE cc_start: 0.8478 (t80) cc_final: 0.8213 (t80) REVERT: R 124 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8199 (mm) REVERT: R 250 PHE cc_start: 0.7077 (m-10) cc_final: 0.6835 (m-10) REVERT: R 257 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8153 (p) REVERT: R 278 LEU cc_start: 0.8214 (mm) cc_final: 0.7936 (mt) REVERT: S 78 THR cc_start: 0.8258 (t) cc_final: 0.8001 (p) REVERT: S 148 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6874 (ttm170) REVERT: S 154 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7864 (tp) REVERT: S 185 SER cc_start: 0.8379 (m) cc_final: 0.8083 (p) outliers start: 45 outliers final: 34 residues processed: 235 average time/residue: 0.2432 time to fit residues: 75.3814 Evaluate side-chains 252 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 306 GLN A 333 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.183 Angle : 0.472 6.479 12425 Z= 0.256 Chirality : 0.040 0.189 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.580 52.887 1252 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.15 % Allowed : 22.77 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1125 helix: 2.60 (0.25), residues: 407 sheet: 0.47 (0.30), residues: 280 loop : -0.40 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS B 91 PHE 0.019 0.001 PHE R 214 TYR 0.020 0.001 TYR S 223 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7456 (mpp) cc_final: 0.7175 (mmm) REVERT: A 298 GLU cc_start: 0.6648 (tp30) cc_final: 0.6292 (tp30) REVERT: A 317 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8027 (ptpp) REVERT: A 345 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7866 (mptt) REVERT: B 19 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.7011 (mtm-85) REVERT: B 134 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7554 (ttp80) REVERT: B 137 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7900 (tpp80) REVERT: B 197 ARG cc_start: 0.6990 (mpt-90) cc_final: 0.6540 (mpt-90) REVERT: B 251 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8364 (mtt90) REVERT: B 263 THR cc_start: 0.8281 (p) cc_final: 0.7718 (m) REVERT: B 301 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7969 (mtpp) REVERT: B 335 PHE cc_start: 0.8474 (m-80) cc_final: 0.8082 (m-80) REVERT: R 46 PHE cc_start: 0.8462 (t80) cc_final: 0.8185 (t80) REVERT: R 72 VAL cc_start: 0.8117 (t) cc_final: 0.7867 (p) REVERT: R 124 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8233 (mm) REVERT: R 208 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7876 (mt) REVERT: R 250 PHE cc_start: 0.7030 (m-10) cc_final: 0.6821 (m-10) REVERT: R 257 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8144 (p) REVERT: R 278 LEU cc_start: 0.8181 (mm) cc_final: 0.7841 (mt) REVERT: S 6 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6911 (mt-10) REVERT: S 78 THR cc_start: 0.8239 (t) cc_final: 0.7989 (p) REVERT: S 148 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6943 (ttm170) REVERT: S 154 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7928 (tp) REVERT: S 185 SER cc_start: 0.8370 (m) cc_final: 0.8067 (p) outliers start: 41 outliers final: 30 residues processed: 234 average time/residue: 0.2440 time to fit residues: 76.2711 Evaluate side-chains 248 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 106 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9182 Z= 0.189 Angle : 0.474 6.738 12425 Z= 0.257 Chirality : 0.040 0.189 1414 Planarity : 0.004 0.054 1556 Dihedral : 4.533 53.284 1252 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.76 % Allowed : 22.47 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1125 helix: 2.64 (0.25), residues: 407 sheet: 0.48 (0.31), residues: 280 loop : -0.42 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.002 0.001 HIS A 213 PHE 0.020 0.001 PHE R 214 TYR 0.022 0.001 TYR S 223 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7465 (mpp) cc_final: 0.7182 (mmm) REVERT: A 262 THR cc_start: 0.8314 (m) cc_final: 0.8098 (m) REVERT: A 298 GLU cc_start: 0.6603 (tp30) cc_final: 0.6253 (tp30) REVERT: A 317 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8057 (ptpp) REVERT: A 345 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7865 (mptt) REVERT: B 19 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.6870 (mtm-85) REVERT: B 134 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7548 (ttp80) REVERT: B 137 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7957 (tpp80) REVERT: B 197 ARG cc_start: 0.6999 (mpt-90) cc_final: 0.6526 (mpt-90) REVERT: B 262 MET cc_start: 0.7955 (ptm) cc_final: 0.7179 (ptm) REVERT: B 263 THR cc_start: 0.8328 (p) cc_final: 0.7926 (m) REVERT: B 301 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8064 (mtpp) REVERT: B 325 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: B 335 PHE cc_start: 0.8476 (m-80) cc_final: 0.8062 (m-80) REVERT: R 57 ILE cc_start: 0.8129 (mt) cc_final: 0.7857 (mm) REVERT: R 72 VAL cc_start: 0.8112 (t) cc_final: 0.7866 (p) REVERT: R 124 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8140 (mm) REVERT: R 250 PHE cc_start: 0.7030 (m-10) cc_final: 0.6818 (m-10) REVERT: R 257 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (p) REVERT: R 278 LEU cc_start: 0.8176 (mm) cc_final: 0.7827 (mt) REVERT: S 6 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: S 78 THR cc_start: 0.8241 (t) cc_final: 0.7992 (p) REVERT: S 148 ARG cc_start: 0.7214 (ttm110) cc_final: 0.6930 (ttm170) REVERT: S 185 SER cc_start: 0.8371 (m) cc_final: 0.8074 (p) outliers start: 47 outliers final: 34 residues processed: 236 average time/residue: 0.2601 time to fit residues: 79.8159 Evaluate side-chains 257 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 306 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.217 Angle : 0.485 7.224 12425 Z= 0.262 Chirality : 0.040 0.198 1414 Planarity : 0.004 0.054 1556 Dihedral : 4.551 52.469 1252 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.35 % Allowed : 23.18 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1125 helix: 2.63 (0.25), residues: 407 sheet: 0.44 (0.31), residues: 280 loop : -0.45 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.021 0.001 PHE R 214 TYR 0.022 0.001 TYR S 223 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7494 (mpp) cc_final: 0.7171 (mmm) REVERT: A 298 GLU cc_start: 0.6585 (tp30) cc_final: 0.6245 (tp30) REVERT: A 345 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7865 (mptt) REVERT: B 85 TYR cc_start: 0.8692 (m-10) cc_final: 0.8441 (m-10) REVERT: B 134 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7541 (ttp80) REVERT: B 137 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7972 (tpp80) REVERT: B 197 ARG cc_start: 0.7004 (mpt-90) cc_final: 0.6508 (mpt-90) REVERT: B 262 MET cc_start: 0.8016 (ptm) cc_final: 0.7223 (ptm) REVERT: B 263 THR cc_start: 0.8230 (p) cc_final: 0.8003 (m) REVERT: B 301 LYS cc_start: 0.8295 (mtpt) cc_final: 0.8070 (mtpp) REVERT: B 325 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7483 (mtm) REVERT: B 335 PHE cc_start: 0.8486 (m-80) cc_final: 0.8075 (m-80) REVERT: R 103 THR cc_start: 0.8121 (p) cc_final: 0.7785 (t) REVERT: R 124 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (mm) REVERT: R 257 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8145 (p) REVERT: R 278 LEU cc_start: 0.8184 (mm) cc_final: 0.7830 (mt) REVERT: S 6 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: S 78 THR cc_start: 0.8244 (t) cc_final: 0.8005 (p) REVERT: S 148 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6955 (ttm170) REVERT: S 185 SER cc_start: 0.8372 (m) cc_final: 0.8077 (p) outliers start: 43 outliers final: 33 residues processed: 243 average time/residue: 0.2506 time to fit residues: 79.9129 Evaluate side-chains 261 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0050 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.163 Angle : 0.470 7.258 12425 Z= 0.253 Chirality : 0.040 0.195 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.477 53.133 1252 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.85 % Allowed : 23.99 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1125 helix: 2.68 (0.25), residues: 407 sheet: 0.48 (0.31), residues: 280 loop : -0.41 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS R 292 PHE 0.020 0.001 PHE R 117 TYR 0.014 0.001 TYR S 223 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7472 (mpp) cc_final: 0.7154 (mmm) REVERT: A 298 GLU cc_start: 0.6618 (tp30) cc_final: 0.6342 (tp30) REVERT: A 345 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7870 (mptt) REVERT: B 85 TYR cc_start: 0.8652 (m-10) cc_final: 0.8393 (m-10) REVERT: B 134 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7548 (ttp80) REVERT: B 137 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7954 (tpp80) REVERT: B 197 ARG cc_start: 0.7022 (mpt-90) cc_final: 0.6543 (mpt-90) REVERT: B 262 MET cc_start: 0.8001 (ptm) cc_final: 0.7271 (ptm) REVERT: B 263 THR cc_start: 0.8285 (p) cc_final: 0.8004 (m) REVERT: B 301 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8064 (mtpp) REVERT: B 335 PHE cc_start: 0.8473 (m-80) cc_final: 0.8070 (m-80) REVERT: R 72 VAL cc_start: 0.8090 (t) cc_final: 0.7884 (p) REVERT: R 103 THR cc_start: 0.8106 (p) cc_final: 0.7755 (t) REVERT: R 183 CYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5704 (t) REVERT: R 250 PHE cc_start: 0.6885 (m-10) cc_final: 0.6677 (m-10) REVERT: R 257 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8139 (p) REVERT: R 278 LEU cc_start: 0.8160 (mm) cc_final: 0.7804 (mt) REVERT: S 34 MET cc_start: 0.8246 (mmm) cc_final: 0.8026 (mmm) REVERT: S 78 THR cc_start: 0.8232 (t) cc_final: 0.7993 (p) REVERT: S 148 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6927 (ttm170) REVERT: S 185 SER cc_start: 0.8371 (m) cc_final: 0.8065 (p) outliers start: 38 outliers final: 30 residues processed: 244 average time/residue: 0.2435 time to fit residues: 78.2332 Evaluate side-chains 259 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.190 Angle : 0.483 7.395 12425 Z= 0.260 Chirality : 0.040 0.197 1414 Planarity : 0.004 0.054 1556 Dihedral : 4.496 52.690 1252 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.44 % Allowed : 24.19 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1125 helix: 2.67 (0.25), residues: 407 sheet: 0.47 (0.31), residues: 280 loop : -0.43 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.003 0.001 HIS R 264 PHE 0.023 0.001 PHE R 117 TYR 0.016 0.001 TYR S 223 ARG 0.005 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7482 (mpp) cc_final: 0.7167 (mmm) REVERT: A 298 GLU cc_start: 0.6616 (tp30) cc_final: 0.6349 (tp30) REVERT: A 345 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7864 (mptt) REVERT: B 19 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6870 (mtm-85) REVERT: B 85 TYR cc_start: 0.8673 (m-10) cc_final: 0.8421 (m-10) REVERT: B 134 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7529 (ttp80) REVERT: B 137 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7955 (tpp80) REVERT: B 197 ARG cc_start: 0.7036 (mpt-90) cc_final: 0.6594 (mpt-90) REVERT: B 262 MET cc_start: 0.8028 (ptm) cc_final: 0.7332 (ptm) REVERT: B 263 THR cc_start: 0.8306 (p) cc_final: 0.8017 (m) REVERT: B 301 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8083 (mtpp) REVERT: B 335 PHE cc_start: 0.8478 (m-80) cc_final: 0.8068 (m-80) REVERT: R 72 VAL cc_start: 0.8100 (t) cc_final: 0.7884 (p) REVERT: R 103 THR cc_start: 0.8105 (p) cc_final: 0.7766 (t) REVERT: R 257 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8143 (p) REVERT: R 278 LEU cc_start: 0.8154 (mm) cc_final: 0.7791 (mt) REVERT: S 34 MET cc_start: 0.8215 (mmm) cc_final: 0.8003 (mmm) REVERT: S 78 THR cc_start: 0.8226 (t) cc_final: 0.7990 (p) REVERT: S 148 ARG cc_start: 0.7232 (ttm110) cc_final: 0.6951 (ttm170) REVERT: S 185 SER cc_start: 0.8382 (m) cc_final: 0.8080 (p) outliers start: 34 outliers final: 33 residues processed: 242 average time/residue: 0.2400 time to fit residues: 76.7690 Evaluate side-chains 263 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110713 restraints weight = 13609.904| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.14 r_work: 0.3296 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9182 Z= 0.257 Angle : 0.508 7.818 12425 Z= 0.275 Chirality : 0.041 0.212 1414 Planarity : 0.004 0.054 1556 Dihedral : 4.593 51.257 1252 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.95 % Allowed : 24.39 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1125 helix: 2.59 (0.25), residues: 407 sheet: 0.42 (0.31), residues: 281 loop : -0.50 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.025 0.002 PHE R 117 TYR 0.017 0.002 TYR S 223 ARG 0.005 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.96 seconds wall clock time: 45 minutes 0.82 seconds (2700.82 seconds total)