Starting phenix.real_space_refine on Thu Feb 13 11:51:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwl_37892/02_2025/8wwl_37892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwl_37892/02_2025/8wwl_37892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwl_37892/02_2025/8wwl_37892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwl_37892/02_2025/8wwl_37892.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwl_37892/02_2025/8wwl_37892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwl_37892/02_2025/8wwl_37892.cif" } resolution = 2.78 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= 0.070 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 68 5.16 5 C 5708 2.51 5 N 1518 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8964 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2239 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.41, per 1000 atoms: 0.60 Number of scatterers: 8964 At special positions: 0 Unit cell: (87.74, 119.84, 120.91, 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 68 16.00 O 1670 8.00 N 1518 7.00 C 5708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 38.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.596A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.590A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.044A 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 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.763A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.635A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.522A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 108 through 137 removed outlier: 3.638A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 removed outlier: 3.553A pdb=" N SER R 155 " --> pdb=" O ILE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 174 removed outlier: 3.605A pdb=" N MET R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 4.018A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.797A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.583A pdb=" N TYR R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.720A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.089A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix removed outlier: 3.542A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.345A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.562A 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: 5.734A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.609A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.140A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.720A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.647A 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: 6.941A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.402A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.974A 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: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.880A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.257A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.209A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.537A pdb=" N VAL L 12 " --> pdb=" O LEU L 9 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1302 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: 3.08 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2890 1.34 - 1.46: 2196 1.46 - 1.58: 3970 1.58 - 1.70: 0 1.70 - 1.81: 99 Bond restraints: 9155 Sorted by residual: bond pdb=" N VAL E 147 " pdb=" CA VAL E 147 " ideal model delta sigma weight residual 1.454 1.461 -0.006 7.70e-03 1.69e+04 6.88e-01 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.57e-01 bond pdb=" CA GLY A 292 " pdb=" C GLY A 292 " ideal model delta sigma weight residual 1.521 1.513 0.008 1.13e-02 7.83e+03 4.84e-01 bond pdb=" N GLY A 292 " pdb=" CA GLY A 292 " ideal model delta sigma weight residual 1.443 1.449 -0.006 8.60e-03 1.35e+04 4.12e-01 bond pdb=" C VAL E 64 " pdb=" O VAL E 64 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.30e-02 5.92e+03 3.91e-01 ... (remaining 9150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 12083 1.02 - 2.04: 281 2.04 - 3.06: 37 3.06 - 4.07: 13 4.07 - 5.09: 10 Bond angle restraints: 12424 Sorted by residual: angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 125.82 -3.08 1.44e+00 4.82e-01 4.59e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.25 -3.71 1.91e+00 2.74e-01 3.77e+00 angle pdb=" CA GLY A 292 " pdb=" C GLY A 292 " pdb=" N SER A 293 " ideal model delta sigma weight residual 114.30 116.61 -2.31 1.20e+00 6.94e-01 3.69e+00 angle pdb=" N GLY B 330 " pdb=" CA GLY B 330 " pdb=" C GLY B 330 " ideal model delta sigma weight residual 112.51 109.17 3.34 1.90e+00 2.77e-01 3.09e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 126.00 -2.53 1.53e+00 4.27e-01 2.74e+00 ... (remaining 12419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.06: 5148 14.06 - 28.12: 211 28.12 - 42.18: 47 42.18 - 56.24: 16 56.24 - 70.30: 4 Dihedral angle restraints: 5426 sinusoidal: 2060 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 5423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 857 0.026 - 0.052: 345 0.052 - 0.078: 126 0.078 - 0.105: 65 0.105 - 0.131: 32 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA VAL E 199 " pdb=" N VAL E 199 " pdb=" C VAL E 199 " pdb=" CB VAL E 199 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1422 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO B 236 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO E 107 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 194 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.016 5.00e-02 4.00e+02 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 188 2.69 - 3.24: 8567 3.24 - 3.79: 14268 3.79 - 4.35: 20357 4.35 - 4.90: 33380 Nonbonded interactions: 76760 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.197 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.274 3.040 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.275 3.120 nonbonded pdb=" O ALA R 364 " pdb=" OG SER R 367 " model vdw 2.278 3.040 ... (remaining 76755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9155 Z= 0.144 Angle : 0.415 5.092 12424 Z= 0.227 Chirality : 0.039 0.131 1425 Planarity : 0.003 0.049 1571 Dihedral : 8.895 70.304 3242 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.83 % Allowed : 3.41 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.49 (0.25), residues: 1144 helix: 0.53 (0.26), residues: 398 sheet: 0.54 (0.30), residues: 291 loop : 0.20 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE B 151 TYR 0.007 0.001 TYR E 103 ARG 0.002 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8280 (mttt) cc_final: 0.8033 (mtpt) REVERT: A 21 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7623 (mtm110) REVERT: A 25 GLU cc_start: 0.7724 (tt0) cc_final: 0.7457 (tm-30) REVERT: A 53 MET cc_start: 0.6223 (mtt) cc_final: 0.5954 (mtt) REVERT: A 186 GLU cc_start: 0.7970 (tt0) cc_final: 0.7752 (mt-10) REVERT: A 319 ILE cc_start: 0.8913 (mt) cc_final: 0.8704 (mm) REVERT: A 349 LYS cc_start: 0.8292 (mttt) cc_final: 0.7789 (mtmt) REVERT: B 96 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7318 (mtt-85) REVERT: B 130 GLU cc_start: 0.7946 (mp0) cc_final: 0.7599 (mt-10) REVERT: B 172 GLU cc_start: 0.7027 (tp30) cc_final: 0.6769 (tp30) REVERT: B 188 MET cc_start: 0.8779 (mmm) cc_final: 0.8261 (mmm) REVERT: B 189 SER cc_start: 0.8231 (p) cc_final: 0.7910 (t) REVERT: E 83 MET cc_start: 0.8883 (mtm) cc_final: 0.8427 (mtp) REVERT: E 85 SER cc_start: 0.8252 (m) cc_final: 0.7889 (t) REVERT: E 90 ASP cc_start: 0.8183 (m-30) cc_final: 0.7978 (m-30) REVERT: R 165 MET cc_start: 0.8508 (ttm) cc_final: 0.8292 (tmm) REVERT: R 191 MET cc_start: 0.7686 (tpt) cc_final: 0.7238 (ttt) REVERT: R 225 LYS cc_start: 0.8284 (mttt) cc_final: 0.8072 (mppt) outliers start: 8 outliers final: 4 residues processed: 191 average time/residue: 1.3475 time to fit residues: 273.1425 Evaluate side-chains 146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 155 ASN B 220 GLN B 259 GLN E 183 GLN R 194 ASN R 281 GLN R 376 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.170577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135166 restraints weight = 9474.985| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.63 r_work: 0.3298 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9155 Z= 0.231 Angle : 0.535 6.427 12424 Z= 0.292 Chirality : 0.043 0.137 1425 Planarity : 0.004 0.049 1571 Dihedral : 5.137 55.310 1259 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 9.40 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.02 (0.25), residues: 1144 helix: 1.71 (0.26), residues: 395 sheet: 0.32 (0.30), residues: 287 loop : 0.13 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 179 PHE 0.016 0.002 PHE A 196 TYR 0.012 0.001 TYR R 341 ARG 0.007 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8303 (mttt) cc_final: 0.7969 (mtpt) REVERT: A 21 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7506 (mtm110) REVERT: A 25 GLU cc_start: 0.7949 (tt0) cc_final: 0.7566 (tt0) REVERT: A 53 MET cc_start: 0.6126 (mtt) cc_final: 0.5800 (mtt) REVERT: A 186 GLU cc_start: 0.8072 (tt0) cc_final: 0.7688 (mt-10) REVERT: A 276 GLU cc_start: 0.7418 (mp0) cc_final: 0.7160 (mp0) REVERT: A 349 LYS cc_start: 0.8102 (mttt) cc_final: 0.7638 (mtpt) REVERT: B 96 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7619 (mtt-85) REVERT: B 130 GLU cc_start: 0.8123 (mp0) cc_final: 0.7654 (mt-10) REVERT: B 146 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 188 MET cc_start: 0.8723 (mmm) cc_final: 0.8292 (mmm) REVERT: B 189 SER cc_start: 0.8192 (p) cc_final: 0.7779 (t) REVERT: B 217 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7031 (pp-130) REVERT: B 219 ARG cc_start: 0.7438 (mmm160) cc_final: 0.6638 (mmt180) REVERT: C 21 MET cc_start: 0.7793 (mmm) cc_final: 0.6949 (ttp) REVERT: E 83 MET cc_start: 0.8849 (mtm) cc_final: 0.8365 (mtp) REVERT: E 179 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: R 169 ILE cc_start: 0.7563 (pt) cc_final: 0.6964 (mm) REVERT: R 191 MET cc_start: 0.7684 (tpt) cc_final: 0.7074 (ttt) REVERT: R 235 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8026 (mt) REVERT: R 315 SER cc_start: 0.6654 (m) cc_final: 0.6241 (p) outliers start: 25 outliers final: 11 residues processed: 156 average time/residue: 1.3660 time to fit residues: 226.2913 Evaluate side-chains 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.169283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133619 restraints weight = 9530.493| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.65 r_work: 0.3280 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9155 Z= 0.274 Angle : 0.536 6.508 12424 Z= 0.288 Chirality : 0.043 0.139 1425 Planarity : 0.004 0.051 1571 Dihedral : 4.877 53.552 1257 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 10.02 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.04 (0.25), residues: 1144 helix: 2.00 (0.26), residues: 394 sheet: 0.16 (0.30), residues: 287 loop : -0.00 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE A 196 TYR 0.011 0.001 TYR E 103 ARG 0.007 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8228 (mttt) cc_final: 0.7949 (mtpt) REVERT: A 21 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7475 (mtm110) REVERT: A 25 GLU cc_start: 0.7919 (tt0) cc_final: 0.7536 (tt0) REVERT: A 186 GLU cc_start: 0.8081 (tt0) cc_final: 0.7678 (mt-10) REVERT: A 276 GLU cc_start: 0.7241 (mp0) cc_final: 0.6934 (mp0) REVERT: A 330 LYS cc_start: 0.7270 (mtmm) cc_final: 0.6052 (tttp) REVERT: A 349 LYS cc_start: 0.8094 (mttt) cc_final: 0.7634 (mtpt) REVERT: B 96 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7620 (mtt-85) REVERT: B 146 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8336 (mp) REVERT: B 188 MET cc_start: 0.8729 (mmm) cc_final: 0.8385 (mmm) REVERT: B 189 SER cc_start: 0.8190 (p) cc_final: 0.7780 (t) REVERT: B 217 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7092 (pp-130) REVERT: B 219 ARG cc_start: 0.7366 (mmm160) cc_final: 0.6618 (mmt180) REVERT: C 21 MET cc_start: 0.7734 (mmm) cc_final: 0.6900 (ttp) REVERT: E 6 GLU cc_start: 0.7438 (mp0) cc_final: 0.7158 (mt-10) REVERT: E 83 MET cc_start: 0.8829 (mtm) cc_final: 0.8423 (mtp) REVERT: E 93 MET cc_start: 0.8822 (ttt) cc_final: 0.8345 (tpp) REVERT: E 179 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: R 121 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7108 (mm) REVERT: R 191 MET cc_start: 0.7651 (tpt) cc_final: 0.7045 (ttt) REVERT: R 235 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8075 (mt) REVERT: R 315 SER cc_start: 0.6755 (m) cc_final: 0.6295 (p) outliers start: 28 outliers final: 14 residues processed: 156 average time/residue: 1.3727 time to fit residues: 227.2425 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 87 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 176 GLN B 268 ASN B 293 ASN E 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.172295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136552 restraints weight = 9499.686| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.62 r_work: 0.3328 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9155 Z= 0.154 Angle : 0.466 6.698 12424 Z= 0.250 Chirality : 0.041 0.137 1425 Planarity : 0.004 0.050 1571 Dihedral : 4.613 59.081 1257 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.20 % Allowed : 10.54 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.23 (0.25), residues: 1144 helix: 2.35 (0.26), residues: 392 sheet: 0.18 (0.30), residues: 284 loop : -0.01 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE A 196 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8258 (mttt) cc_final: 0.7973 (mtmt) REVERT: A 21 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7509 (mtm110) REVERT: A 25 GLU cc_start: 0.7917 (tt0) cc_final: 0.7521 (tt0) REVERT: A 186 GLU cc_start: 0.7959 (tt0) cc_final: 0.7648 (mt-10) REVERT: A 209 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7576 (pttp) REVERT: A 276 GLU cc_start: 0.7178 (mp0) cc_final: 0.6872 (mp0) REVERT: A 330 LYS cc_start: 0.7222 (mtmm) cc_final: 0.5904 (tttp) REVERT: A 349 LYS cc_start: 0.8037 (mttt) cc_final: 0.7523 (ttmt) REVERT: B 96 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7611 (mtt-85) REVERT: B 130 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 188 MET cc_start: 0.8690 (mmm) cc_final: 0.8326 (mmm) REVERT: B 189 SER cc_start: 0.8145 (p) cc_final: 0.7748 (t) REVERT: B 274 THR cc_start: 0.8587 (p) cc_final: 0.8176 (p) REVERT: C 21 MET cc_start: 0.7759 (mmm) cc_final: 0.6971 (ttp) REVERT: E 83 MET cc_start: 0.8780 (mtm) cc_final: 0.8346 (mtp) REVERT: E 93 MET cc_start: 0.8813 (ttt) cc_final: 0.8273 (tpp) REVERT: E 179 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: R 136 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7353 (tptt) REVERT: R 184 MET cc_start: 0.6963 (mmm) cc_final: 0.6642 (tpt) REVERT: R 191 MET cc_start: 0.7401 (tpt) cc_final: 0.6818 (ttt) REVERT: R 235 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8149 (mt) REVERT: R 315 SER cc_start: 0.6511 (m) cc_final: 0.6095 (p) outliers start: 31 outliers final: 15 residues processed: 158 average time/residue: 1.4026 time to fit residues: 234.5929 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 59 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 0.0370 chunk 5 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.172324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136679 restraints weight = 9517.478| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.62 r_work: 0.3322 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9155 Z= 0.157 Angle : 0.466 6.806 12424 Z= 0.248 Chirality : 0.041 0.136 1425 Planarity : 0.003 0.049 1571 Dihedral : 4.566 58.741 1257 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.10 % Allowed : 10.33 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.28 (0.25), residues: 1144 helix: 2.46 (0.26), residues: 395 sheet: 0.17 (0.30), residues: 284 loop : -0.06 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8219 (mttt) cc_final: 0.7959 (mtmt) REVERT: A 21 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7549 (mtm110) REVERT: A 25 GLU cc_start: 0.7938 (tt0) cc_final: 0.7510 (tm-30) REVERT: A 186 GLU cc_start: 0.7957 (tt0) cc_final: 0.7649 (mt-10) REVERT: A 330 LYS cc_start: 0.7305 (mtmm) cc_final: 0.5963 (tttp) REVERT: A 349 LYS cc_start: 0.8015 (mttt) cc_final: 0.7540 (ttmt) REVERT: B 96 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7636 (mtt-85) REVERT: B 130 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 188 MET cc_start: 0.8677 (mmm) cc_final: 0.8307 (mmm) REVERT: B 189 SER cc_start: 0.8097 (p) cc_final: 0.7684 (t) REVERT: B 274 THR cc_start: 0.8590 (p) cc_final: 0.8235 (p) REVERT: C 21 MET cc_start: 0.7752 (mmm) cc_final: 0.6855 (ttm) REVERT: E 83 MET cc_start: 0.8747 (mtm) cc_final: 0.8210 (mtp) REVERT: E 93 MET cc_start: 0.8795 (ttt) cc_final: 0.8273 (tpp) REVERT: R 136 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7340 (tptt) REVERT: R 139 LYS cc_start: 0.8020 (mttt) cc_final: 0.7815 (mtpt) REVERT: R 183 THR cc_start: 0.7438 (m) cc_final: 0.7167 (p) REVERT: R 184 MET cc_start: 0.7039 (mmm) cc_final: 0.6747 (tpt) REVERT: R 191 MET cc_start: 0.7425 (tpt) cc_final: 0.6824 (ttt) REVERT: R 235 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8180 (mt) REVERT: R 345 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8082 (tp40) outliers start: 30 outliers final: 15 residues processed: 156 average time/residue: 1.4030 time to fit residues: 231.7741 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 39 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.172789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137101 restraints weight = 9520.265| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.62 r_work: 0.3332 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9155 Z= 0.154 Angle : 0.472 8.505 12424 Z= 0.248 Chirality : 0.041 0.139 1425 Planarity : 0.003 0.048 1571 Dihedral : 4.512 56.941 1257 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.89 % Allowed : 10.54 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1144 helix: 2.52 (0.26), residues: 395 sheet: 0.18 (0.30), residues: 285 loop : -0.07 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.009 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.950 Fit side-chains REVERT: A 17 LYS cc_start: 0.8200 (mttt) cc_final: 0.7931 (mtmt) REVERT: A 21 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7568 (mtm110) REVERT: A 25 GLU cc_start: 0.7934 (tt0) cc_final: 0.7505 (tm-30) REVERT: A 186 GLU cc_start: 0.7956 (tt0) cc_final: 0.7640 (mt-10) REVERT: A 276 GLU cc_start: 0.7179 (mp0) cc_final: 0.6902 (mp0) REVERT: A 330 LYS cc_start: 0.7280 (mtmm) cc_final: 0.5954 (tttp) REVERT: A 349 LYS cc_start: 0.8003 (mttt) cc_final: 0.7535 (ttmt) REVERT: B 96 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7631 (mtt-85) REVERT: B 130 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 137 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7331 (ttm-80) REVERT: B 188 MET cc_start: 0.8665 (mmm) cc_final: 0.8295 (mmm) REVERT: B 189 SER cc_start: 0.8107 (p) cc_final: 0.7689 (t) REVERT: B 274 THR cc_start: 0.8572 (p) cc_final: 0.8231 (p) REVERT: C 21 MET cc_start: 0.7776 (mmm) cc_final: 0.6879 (ttp) REVERT: E 83 MET cc_start: 0.8754 (mtm) cc_final: 0.8242 (mtp) REVERT: E 93 MET cc_start: 0.8761 (ttt) cc_final: 0.8396 (tpp) REVERT: R 136 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7344 (mptt) REVERT: R 184 MET cc_start: 0.6985 (mmm) cc_final: 0.6613 (tpt) REVERT: R 191 MET cc_start: 0.7419 (tpt) cc_final: 0.6810 (ttt) REVERT: R 235 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8184 (mt) REVERT: R 332 LEU cc_start: 0.8049 (mt) cc_final: 0.7800 (tp) outliers start: 28 outliers final: 18 residues processed: 152 average time/residue: 1.4117 time to fit residues: 227.7410 Evaluate side-chains 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN E 186 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.168641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132240 restraints weight = 9554.830| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.70 r_work: 0.3272 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9155 Z= 0.321 Angle : 0.555 7.055 12424 Z= 0.294 Chirality : 0.044 0.144 1425 Planarity : 0.004 0.048 1571 Dihedral : 4.945 56.902 1257 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.20 % Allowed : 10.64 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.08 (0.25), residues: 1144 helix: 2.27 (0.26), residues: 397 sheet: 0.10 (0.30), residues: 289 loop : -0.17 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 339 HIS 0.004 0.001 HIS E 35 PHE 0.019 0.002 PHE A 196 TYR 0.013 0.002 TYR E 103 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.002 Fit side-chains REVERT: A 17 LYS cc_start: 0.8272 (mttt) cc_final: 0.7999 (mtpt) REVERT: A 21 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7603 (mtm110) REVERT: A 25 GLU cc_start: 0.8009 (tt0) cc_final: 0.7616 (tm-30) REVERT: A 186 GLU cc_start: 0.8021 (tt0) cc_final: 0.7675 (mt-10) REVERT: A 276 GLU cc_start: 0.7200 (mp0) cc_final: 0.6908 (mp0) REVERT: A 330 LYS cc_start: 0.7548 (mtmm) cc_final: 0.6171 (tttp) REVERT: A 349 LYS cc_start: 0.8089 (mttt) cc_final: 0.7618 (ttmt) REVERT: B 96 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7693 (mtt-85) REVERT: B 137 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7551 (ttm-80) REVERT: B 146 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 188 MET cc_start: 0.8719 (mmm) cc_final: 0.8278 (mmm) REVERT: B 189 SER cc_start: 0.8176 (p) cc_final: 0.7780 (t) REVERT: C 21 MET cc_start: 0.7908 (mmm) cc_final: 0.7091 (ttp) REVERT: E 93 MET cc_start: 0.8854 (ttt) cc_final: 0.8486 (tpp) REVERT: R 183 THR cc_start: 0.7455 (m) cc_final: 0.7184 (p) REVERT: R 184 MET cc_start: 0.7204 (mmm) cc_final: 0.6960 (tpt) REVERT: R 191 MET cc_start: 0.7532 (tpt) cc_final: 0.6959 (ttt) REVERT: R 235 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8163 (mt) REVERT: R 345 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8177 (tp40) outliers start: 31 outliers final: 20 residues processed: 152 average time/residue: 1.3908 time to fit residues: 224.4215 Evaluate side-chains 150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN E 186 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134684 restraints weight = 9641.556| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.68 r_work: 0.3290 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9155 Z= 0.210 Angle : 0.505 7.272 12424 Z= 0.268 Chirality : 0.042 0.145 1425 Planarity : 0.004 0.049 1571 Dihedral : 4.839 59.588 1257 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.31 % Allowed : 10.85 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.14 (0.25), residues: 1144 helix: 2.35 (0.26), residues: 397 sheet: 0.16 (0.30), residues: 283 loop : -0.20 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 189 TYR 0.011 0.001 TYR R 342 ARG 0.009 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8185 (mttt) cc_final: 0.7915 (mtpt) REVERT: A 21 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7464 (mtm110) REVERT: A 25 GLU cc_start: 0.7895 (tt0) cc_final: 0.7505 (tm-30) REVERT: A 186 GLU cc_start: 0.7994 (tt0) cc_final: 0.7667 (mt-10) REVERT: A 330 LYS cc_start: 0.7419 (mtmm) cc_final: 0.6086 (tttp) REVERT: A 349 LYS cc_start: 0.8013 (mttt) cc_final: 0.7529 (ttmt) REVERT: B 96 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7646 (mtt-85) REVERT: B 137 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7595 (ttm-80) REVERT: B 146 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 188 MET cc_start: 0.8690 (mmm) cc_final: 0.8251 (mmm) REVERT: B 189 SER cc_start: 0.8172 (p) cc_final: 0.7763 (t) REVERT: B 217 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6960 (pp-130) REVERT: B 219 ARG cc_start: 0.7366 (mmm160) cc_final: 0.6598 (mmt180) REVERT: C 21 MET cc_start: 0.7861 (mmm) cc_final: 0.6981 (ttp) REVERT: E 83 MET cc_start: 0.8888 (mtm) cc_final: 0.8383 (mtp) REVERT: E 93 MET cc_start: 0.8835 (ttt) cc_final: 0.8453 (tpp) REVERT: E 179 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: E 186 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7996 (pp30) REVERT: R 169 ILE cc_start: 0.7416 (pt) cc_final: 0.6739 (mm) REVERT: R 183 THR cc_start: 0.7315 (m) cc_final: 0.7072 (p) REVERT: R 184 MET cc_start: 0.7170 (mmm) cc_final: 0.6913 (tpt) REVERT: R 191 MET cc_start: 0.7428 (tpt) cc_final: 0.6896 (ttt) REVERT: R 235 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (mt) REVERT: R 345 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8074 (tp40) outliers start: 32 outliers final: 20 residues processed: 150 average time/residue: 1.5082 time to fit residues: 239.1313 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN E 186 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.170492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134869 restraints weight = 9524.447| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.61 r_work: 0.3303 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9155 Z= 0.216 Angle : 0.509 7.402 12424 Z= 0.269 Chirality : 0.042 0.140 1425 Planarity : 0.004 0.049 1571 Dihedral : 4.836 59.731 1257 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.89 % Allowed : 11.47 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.15 (0.25), residues: 1144 helix: 2.37 (0.26), residues: 397 sheet: 0.14 (0.30), residues: 282 loop : -0.19 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 189 TYR 0.011 0.001 TYR R 342 ARG 0.009 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8192 (mttt) cc_final: 0.7926 (mtpt) REVERT: A 21 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7478 (mtm110) REVERT: A 25 GLU cc_start: 0.7896 (tt0) cc_final: 0.7505 (tm-30) REVERT: A 186 GLU cc_start: 0.7988 (tt0) cc_final: 0.7657 (mt-10) REVERT: A 330 LYS cc_start: 0.7398 (mtmm) cc_final: 0.6070 (tttp) REVERT: A 349 LYS cc_start: 0.8005 (mttt) cc_final: 0.7533 (ttmt) REVERT: B 96 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7658 (mtt-85) REVERT: B 137 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7637 (ttm-80) REVERT: B 146 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 188 MET cc_start: 0.8690 (mmm) cc_final: 0.8245 (mmm) REVERT: B 189 SER cc_start: 0.8159 (p) cc_final: 0.7748 (t) REVERT: B 217 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6951 (pp-130) REVERT: B 219 ARG cc_start: 0.7364 (mmm160) cc_final: 0.6603 (mmt180) REVERT: C 21 MET cc_start: 0.7851 (mmm) cc_final: 0.6973 (ttp) REVERT: E 83 MET cc_start: 0.8900 (mtm) cc_final: 0.8395 (mtp) REVERT: E 93 MET cc_start: 0.8780 (ttt) cc_final: 0.8429 (tpp) REVERT: E 179 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: R 183 THR cc_start: 0.7319 (m) cc_final: 0.7092 (p) REVERT: R 184 MET cc_start: 0.7160 (mmm) cc_final: 0.6904 (tpt) REVERT: R 191 MET cc_start: 0.7428 (tpt) cc_final: 0.6895 (ttt) REVERT: R 235 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8169 (mt) REVERT: R 325 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6794 (ttp80) REVERT: R 345 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (tp40) outliers start: 28 outliers final: 20 residues processed: 146 average time/residue: 1.4649 time to fit residues: 226.3320 Evaluate side-chains 150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 97 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN B 293 ASN E 186 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.171516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136243 restraints weight = 9560.102| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.60 r_work: 0.3316 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9155 Z= 0.176 Angle : 0.496 7.638 12424 Z= 0.262 Chirality : 0.041 0.158 1425 Planarity : 0.004 0.049 1571 Dihedral : 4.742 58.087 1257 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.79 % Allowed : 11.78 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.23 (0.25), residues: 1144 helix: 2.49 (0.26), residues: 395 sheet: 0.18 (0.30), residues: 287 loop : -0.18 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.010 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8171 (mttt) cc_final: 0.7912 (mtpt) REVERT: A 21 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7501 (mtm110) REVERT: A 25 GLU cc_start: 0.7882 (tt0) cc_final: 0.7488 (tm-30) REVERT: A 186 GLU cc_start: 0.7987 (tt0) cc_final: 0.7664 (mt-10) REVERT: A 330 LYS cc_start: 0.7352 (mtmm) cc_final: 0.6031 (tttp) REVERT: A 349 LYS cc_start: 0.7993 (mttt) cc_final: 0.7520 (ttmt) REVERT: B 96 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7648 (mtt-85) REVERT: B 130 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 146 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 188 MET cc_start: 0.8679 (mmm) cc_final: 0.8226 (mmm) REVERT: B 189 SER cc_start: 0.8116 (p) cc_final: 0.7699 (t) REVERT: B 217 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6941 (pp-130) REVERT: B 219 ARG cc_start: 0.7396 (mmm160) cc_final: 0.6621 (mmt180) REVERT: C 21 MET cc_start: 0.7731 (mmm) cc_final: 0.6800 (ttp) REVERT: E 11 LEU cc_start: 0.8529 (tp) cc_final: 0.8234 (tt) REVERT: E 83 MET cc_start: 0.8878 (mtm) cc_final: 0.8372 (mtp) REVERT: E 93 MET cc_start: 0.8741 (ttt) cc_final: 0.8451 (tpp) REVERT: E 179 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: R 184 MET cc_start: 0.7030 (mmm) cc_final: 0.6685 (tpt) REVERT: R 191 MET cc_start: 0.7401 (tpt) cc_final: 0.6850 (ttt) REVERT: R 235 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8191 (mt) REVERT: R 345 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7993 (tp40) outliers start: 27 outliers final: 18 residues processed: 144 average time/residue: 1.4903 time to fit residues: 227.3850 Evaluate side-chains 145 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134813 restraints weight = 9553.013| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.64 r_work: 0.3301 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9155 Z= 0.240 Angle : 0.529 7.475 12424 Z= 0.278 Chirality : 0.043 0.158 1425 Planarity : 0.004 0.048 1571 Dihedral : 4.850 59.499 1257 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.69 % Allowed : 11.98 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.13 (0.25), residues: 1144 helix: 2.37 (0.26), residues: 397 sheet: 0.11 (0.30), residues: 282 loop : -0.20 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE A 196 TYR 0.011 0.001 TYR E 103 ARG 0.009 0.001 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7419.85 seconds wall clock time: 131 minutes 35.27 seconds (7895.27 seconds total)