Starting phenix.real_space_refine on Tue Mar 3 20:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1f_33562/03_2026/7y1f_33562.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1f_33562/03_2026/7y1f_33562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2026/7y1f_33562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2026/7y1f_33562.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2026/7y1f_33562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2026/7y1f_33562.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 60 5.16 5 C 5561 2.51 5 N 1480 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2256 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8691 At special positions: 0 Unit cell: (102.6, 112.32, 135, 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 60 16.00 O 1590 8.00 N 1480 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 233 " - pdb=" SG CYS R 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 0.59 Conformation dependent library (CDL) restraints added in 377.7 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 35.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.238A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.575A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.208A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.571A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.979A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.971A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'R' and resid 159 through 189 Processing helix chain 'R' and resid 194 through 212 removed outlier: 3.768A pdb=" N ILE R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 removed outlier: 4.097A pdb=" N VAL R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 264 removed outlier: 3.568A pdb=" N HIS R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 272 removed outlier: 4.019A pdb=" N LEU R 269 " --> pdb=" O PRO R 265 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP R 270 " --> pdb=" O VAL R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 298 removed outlier: 4.137A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 337 Processing helix chain 'R' and resid 337 through 357 removed outlier: 4.213A pdb=" N SER R 357 " --> pdb=" O LEU R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 399 removed outlier: 3.782A pdb=" N ASP R 368 " --> pdb=" O SER R 364 " (cutoff:3.500A) Proline residue: R 391 - end of helix Processing helix chain 'R' and resid 409 through 433 removed outlier: 4.344A pdb=" N SER R 413 " --> pdb=" O ALA R 409 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) Proline residue: R 429 - end of helix Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.965A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.859A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.615A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.519A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.545A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.392A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 removed outlier: 5.654A pdb=" N PHE A 223 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 299 through 302 removed outlier: 3.794A pdb=" N GLY R 300 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 313 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 311 " --> pdb=" O LYS R 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.696A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.167A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.470A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.690A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.700A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.777A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.137A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1131 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: 1.50 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2767 1.34 - 1.47: 2247 1.47 - 1.59: 3770 1.59 - 1.72: 0 1.72 - 1.84: 87 Bond restraints: 8871 Sorted by residual: bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.335 1.247 0.087 3.04e-02 1.08e+03 8.23e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.49e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.45e+00 bond pdb=" CG1 ILE B 338 " pdb=" CD1 ILE B 338 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.29e+00 bond pdb=" CB VAL B 112 " pdb=" CG1 VAL B 112 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 8866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 11807 3.38 - 6.75: 200 6.75 - 10.13: 26 10.13 - 13.50: 1 13.50 - 16.88: 1 Bond angle restraints: 12035 Sorted by residual: angle pdb=" C GLU R 305 " pdb=" N ASP R 306 " pdb=" CA ASP R 306 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" CA LEU A 353 " pdb=" CB LEU A 353 " pdb=" CG LEU A 353 " ideal model delta sigma weight residual 116.30 133.18 -16.88 3.50e+00 8.16e-02 2.33e+01 angle pdb=" C ALA E 209 " pdb=" N GLU E 210 " pdb=" CA GLU E 210 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ASP B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 128.70 -5.96 1.44e+00 4.82e-01 1.71e+01 angle pdb=" C ASP B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta sigma weight residual 120.60 127.21 -6.61 1.60e+00 3.91e-01 1.71e+01 ... (remaining 12030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4701 17.11 - 34.23: 435 34.23 - 51.34: 93 51.34 - 68.45: 8 68.45 - 85.57: 10 Dihedral angle restraints: 5247 sinusoidal: 1964 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.63 -77.63 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N ALA A 11 " pdb=" CA ALA A 11 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1214 0.084 - 0.169: 164 0.169 - 0.253: 16 0.253 - 0.338: 2 0.338 - 0.422: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1395 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.032 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" CG TRP B 332 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 214 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO R 215 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.021 2.00e-02 2.50e+03 1.90e-02 7.22e+00 pdb=" CG TYR B 105 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.001 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1297 2.75 - 3.29: 8569 3.29 - 3.83: 14672 3.83 - 4.36: 17392 4.36 - 4.90: 30149 Nonbonded interactions: 72079 Sorted by model distance: nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.215 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.234 3.040 nonbonded pdb=" O ALA R 419 " pdb=" OG1 THR R 423 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.242 3.040 nonbonded pdb=" O VAL R 386 " pdb=" OG1 THR R 390 " model vdw 2.250 3.040 ... (remaining 72074 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.007 0.099 8875 Z= 0.304 Angle : 1.119 16.879 12043 Z= 0.604 Chirality : 0.060 0.422 1398 Planarity : 0.007 0.098 1505 Dihedral : 13.790 85.567 3117 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.23), residues: 1113 helix: -1.02 (0.24), residues: 357 sheet: -1.36 (0.33), residues: 251 loop : -1.81 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG B 134 TYR 0.047 0.003 TYR B 105 PHE 0.034 0.003 PHE A 323 TRP 0.070 0.004 TRP B 332 HIS 0.013 0.003 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 8871) covalent geometry : angle 1.11796 (12035) SS BOND : bond 0.00816 ( 4) SS BOND : angle 1.91671 ( 8) hydrogen bonds : bond 0.19342 ( 394) hydrogen bonds : angle 7.86503 ( 1131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.312 Fit side-chains REVERT: A 303 ILE cc_start: 0.7538 (mt) cc_final: 0.7302 (mm) REVERT: A 333 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7379 (tp40) REVERT: A 337 ASP cc_start: 0.7943 (m-30) cc_final: 0.7657 (m-30) REVERT: R 214 MET cc_start: 0.6920 (ttm) cc_final: 0.6566 (ttp) REVERT: R 221 TYR cc_start: 0.7337 (t80) cc_final: 0.6872 (t80) REVERT: R 222 LEU cc_start: 0.6161 (mm) cc_final: 0.5681 (mm) REVERT: B 43 ILE cc_start: 0.8389 (mt) cc_final: 0.8067 (mt) REVERT: E 223 TYR cc_start: 0.7885 (m-80) cc_final: 0.7077 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0894 time to fit residues: 28.5552 Evaluate side-chains 197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 322 HIS ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 266 HIS E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.207977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165696 restraints weight = 10384.535| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.46 r_work: 0.3806 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8875 Z= 0.136 Angle : 0.660 9.651 12043 Z= 0.348 Chirality : 0.044 0.257 1398 Planarity : 0.005 0.064 1505 Dihedral : 5.619 24.422 1224 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.73 % Allowed : 9.19 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1113 helix: 0.61 (0.26), residues: 334 sheet: -1.08 (0.33), residues: 249 loop : -1.49 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 32 TYR 0.019 0.002 TYR R 242 PHE 0.031 0.002 PHE R 439 TRP 0.028 0.002 TRP B 332 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8871) covalent geometry : angle 0.66020 (12035) SS BOND : bond 0.00437 ( 4) SS BOND : angle 0.95382 ( 8) hydrogen bonds : bond 0.04359 ( 394) hydrogen bonds : angle 5.31250 ( 1131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 337 ASP cc_start: 0.7970 (m-30) cc_final: 0.7724 (m-30) REVERT: R 187 ILE cc_start: 0.7033 (mm) cc_final: 0.6667 (mt) REVERT: R 214 MET cc_start: 0.6893 (ttm) cc_final: 0.6521 (ttm) REVERT: R 223 MET cc_start: 0.7301 (tmm) cc_final: 0.7089 (ppp) REVERT: R 315 GLN cc_start: 0.5673 (mp10) cc_final: 0.5035 (mp10) REVERT: R 351 MET cc_start: 0.8055 (ttt) cc_final: 0.7800 (ttt) REVERT: B 79 LEU cc_start: 0.8382 (mt) cc_final: 0.8087 (mt) REVERT: B 300 LEU cc_start: 0.8612 (mm) cc_final: 0.8182 (tt) REVERT: C 32 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8093 (mmtm) REVERT: E 47 TRP cc_start: 0.6973 (t60) cc_final: 0.6477 (t60) REVERT: E 179 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6470 (mtm110) REVERT: E 206 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7744 (tpp-160) outliers start: 16 outliers final: 13 residues processed: 221 average time/residue: 0.0941 time to fit residues: 28.3448 Evaluate side-chains 203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 333 GLN ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 424 ASN B 88 ASN B 266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.203944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.161594 restraints weight = 10369.987| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.43 r_work: 0.3793 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8875 Z= 0.165 Angle : 0.669 8.254 12043 Z= 0.350 Chirality : 0.044 0.238 1398 Planarity : 0.004 0.056 1505 Dihedral : 5.435 26.028 1224 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.14 % Allowed : 11.57 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1113 helix: 0.93 (0.26), residues: 337 sheet: -0.94 (0.33), residues: 245 loop : -1.33 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 32 TYR 0.016 0.002 TYR B 105 PHE 0.021 0.002 PHE R 439 TRP 0.016 0.002 TRP B 332 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8871) covalent geometry : angle 0.66840 (12035) SS BOND : bond 0.00445 ( 4) SS BOND : angle 1.00215 ( 8) hydrogen bonds : bond 0.04355 ( 394) hydrogen bonds : angle 5.17893 ( 1131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7483 (tp40) REVERT: A 337 ASP cc_start: 0.8011 (m-30) cc_final: 0.7742 (m-30) REVERT: R 187 ILE cc_start: 0.7073 (mm) cc_final: 0.6707 (mt) REVERT: R 214 MET cc_start: 0.7264 (ttm) cc_final: 0.6817 (ttm) REVERT: R 223 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6931 (ppp) REVERT: R 354 ARG cc_start: 0.7620 (tpp80) cc_final: 0.6101 (tpt90) REVERT: E 47 TRP cc_start: 0.7070 (t60) cc_final: 0.6655 (t60) REVERT: E 93 MET cc_start: 0.6236 (tmm) cc_final: 0.6008 (ptm) REVERT: E 160 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7613 (p) outliers start: 29 outliers final: 21 residues processed: 216 average time/residue: 0.0883 time to fit residues: 26.3640 Evaluate side-chains 209 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.203149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159780 restraints weight = 10593.292| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.45 r_work: 0.3720 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8875 Z= 0.166 Angle : 0.670 8.656 12043 Z= 0.348 Chirality : 0.044 0.256 1398 Planarity : 0.004 0.051 1505 Dihedral : 5.413 26.697 1224 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.35 % Allowed : 15.14 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1113 helix: 1.07 (0.26), residues: 339 sheet: -0.98 (0.32), residues: 257 loop : -1.23 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.015 0.002 TYR B 105 PHE 0.038 0.002 PHE A 323 TRP 0.012 0.002 TRP B 99 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8871) covalent geometry : angle 0.66977 (12035) SS BOND : bond 0.00477 ( 4) SS BOND : angle 0.97294 ( 8) hydrogen bonds : bond 0.04197 ( 394) hydrogen bonds : angle 5.12605 ( 1131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.299 Fit side-chains REVERT: A 247 MET cc_start: 0.7766 (mmp) cc_final: 0.7257 (mmp) REVERT: A 333 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7588 (tp40) REVERT: A 337 ASP cc_start: 0.8049 (m-30) cc_final: 0.7543 (m-30) REVERT: R 187 ILE cc_start: 0.6826 (mm) cc_final: 0.6451 (mt) REVERT: R 214 MET cc_start: 0.7406 (ttm) cc_final: 0.7047 (ttm) REVERT: R 223 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6915 (ppp) REVERT: R 354 ARG cc_start: 0.7707 (tpp80) cc_final: 0.6194 (tpt90) REVERT: B 82 TRP cc_start: 0.7258 (m100) cc_final: 0.6731 (m100) REVERT: B 226 GLU cc_start: 0.7844 (mp0) cc_final: 0.7643 (mm-30) REVERT: C 21 MET cc_start: 0.4092 (tmm) cc_final: 0.3742 (tmm) REVERT: E 47 TRP cc_start: 0.7004 (t60) cc_final: 0.6678 (t60) REVERT: E 93 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6309 (ptm) REVERT: E 160 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7570 (p) REVERT: E 168 ARG cc_start: 0.7117 (mmt90) cc_final: 0.6898 (mmt90) outliers start: 31 outliers final: 25 residues processed: 224 average time/residue: 0.0949 time to fit residues: 29.6199 Evaluate side-chains 226 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 60 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 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 ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.201979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158544 restraints weight = 10548.190| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.45 r_work: 0.3735 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8875 Z= 0.143 Angle : 0.637 7.712 12043 Z= 0.333 Chirality : 0.044 0.239 1398 Planarity : 0.004 0.047 1505 Dihedral : 5.223 25.546 1224 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.68 % Allowed : 16.86 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.25), residues: 1113 helix: 1.20 (0.26), residues: 345 sheet: -0.96 (0.32), residues: 258 loop : -1.14 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.015 0.001 TYR R 242 PHE 0.032 0.002 PHE R 439 TRP 0.010 0.001 TRP B 99 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8871) covalent geometry : angle 0.63716 (12035) SS BOND : bond 0.00420 ( 4) SS BOND : angle 0.84230 ( 8) hydrogen bonds : bond 0.03945 ( 394) hydrogen bonds : angle 4.97584 ( 1131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.333 Fit side-chains REVERT: A 247 MET cc_start: 0.7769 (mmp) cc_final: 0.7384 (mmp) REVERT: A 333 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7767 (tp40) REVERT: A 334 PHE cc_start: 0.7995 (t80) cc_final: 0.7778 (t80) REVERT: A 337 ASP cc_start: 0.7890 (m-30) cc_final: 0.7320 (m-30) REVERT: A 341 ASP cc_start: 0.7966 (m-30) cc_final: 0.7694 (m-30) REVERT: R 187 ILE cc_start: 0.6836 (mm) cc_final: 0.6462 (mt) REVERT: R 214 MET cc_start: 0.7425 (ttm) cc_final: 0.7052 (ttm) REVERT: R 223 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6891 (ppp) REVERT: R 354 ARG cc_start: 0.7743 (tpp80) cc_final: 0.6202 (tpt90) REVERT: B 82 TRP cc_start: 0.7264 (m100) cc_final: 0.6699 (m100) REVERT: B 183 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.7152 (m170) REVERT: B 226 GLU cc_start: 0.7947 (mp0) cc_final: 0.7674 (mm-30) REVERT: E 47 TRP cc_start: 0.7007 (t60) cc_final: 0.6476 (t60) REVERT: E 93 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.6366 (ptm) REVERT: E 160 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7505 (p) outliers start: 34 outliers final: 22 residues processed: 228 average time/residue: 0.0937 time to fit residues: 29.2153 Evaluate side-chains 226 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.0030 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.205585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162798 restraints weight = 10533.678| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.47 r_work: 0.3778 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8875 Z= 0.141 Angle : 0.652 8.964 12043 Z= 0.337 Chirality : 0.044 0.222 1398 Planarity : 0.004 0.045 1505 Dihedral : 5.157 25.376 1224 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.68 % Allowed : 17.73 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1113 helix: 1.31 (0.26), residues: 345 sheet: -0.86 (0.33), residues: 251 loop : -1.12 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.015 0.001 TYR R 242 PHE 0.033 0.002 PHE R 439 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8871) covalent geometry : angle 0.65134 (12035) SS BOND : bond 0.00634 ( 4) SS BOND : angle 1.08986 ( 8) hydrogen bonds : bond 0.03804 ( 394) hydrogen bonds : angle 4.90983 ( 1131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.312 Fit side-chains REVERT: A 333 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7742 (tp40) REVERT: A 337 ASP cc_start: 0.7891 (m-30) cc_final: 0.7277 (m-30) REVERT: A 341 ASP cc_start: 0.8096 (m-30) cc_final: 0.7798 (m-30) REVERT: R 187 ILE cc_start: 0.6804 (mm) cc_final: 0.6516 (mp) REVERT: R 214 MET cc_start: 0.7533 (ttm) cc_final: 0.7208 (ttm) REVERT: R 223 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6795 (tmm) REVERT: R 354 ARG cc_start: 0.7757 (tpp80) cc_final: 0.6266 (tpt90) REVERT: B 82 TRP cc_start: 0.7223 (m100) cc_final: 0.6686 (m100) REVERT: B 183 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7064 (m170) REVERT: B 226 GLU cc_start: 0.7906 (mp0) cc_final: 0.7674 (mm-30) REVERT: C 32 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8178 (tppp) REVERT: E 47 TRP cc_start: 0.6879 (t60) cc_final: 0.6412 (t60) REVERT: E 90 ASP cc_start: 0.5617 (m-30) cc_final: 0.5415 (m-30) outliers start: 34 outliers final: 25 residues processed: 225 average time/residue: 0.0972 time to fit residues: 29.8454 Evaluate side-chains 230 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.0870 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.207798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.164896 restraints weight = 10583.123| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.50 r_work: 0.3831 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8875 Z= 0.131 Angle : 0.651 8.918 12043 Z= 0.333 Chirality : 0.044 0.241 1398 Planarity : 0.004 0.042 1505 Dihedral : 5.033 24.226 1224 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.35 % Allowed : 18.92 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1113 helix: 1.50 (0.27), residues: 344 sheet: -0.80 (0.33), residues: 256 loop : -1.10 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.016 0.001 TYR R 242 PHE 0.034 0.002 PHE R 439 TRP 0.010 0.001 TRP R 324 HIS 0.003 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8871) covalent geometry : angle 0.65093 (12035) SS BOND : bond 0.00497 ( 4) SS BOND : angle 0.96123 ( 8) hydrogen bonds : bond 0.03691 ( 394) hydrogen bonds : angle 4.84917 ( 1131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.335 Fit side-chains REVERT: A 247 MET cc_start: 0.7743 (mmp) cc_final: 0.7169 (mmp) REVERT: A 333 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7753 (tp40) REVERT: A 337 ASP cc_start: 0.7859 (m-30) cc_final: 0.7228 (m-30) REVERT: A 341 ASP cc_start: 0.8122 (m-30) cc_final: 0.7813 (m-30) REVERT: R 183 MET cc_start: 0.5011 (mmt) cc_final: 0.4810 (mmt) REVERT: R 187 ILE cc_start: 0.6785 (mm) cc_final: 0.6500 (mp) REVERT: R 214 MET cc_start: 0.7543 (ttm) cc_final: 0.7231 (ttm) REVERT: R 223 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6994 (tmm) REVERT: R 354 ARG cc_start: 0.7790 (tpp80) cc_final: 0.6268 (tpt90) REVERT: B 82 TRP cc_start: 0.7197 (m100) cc_final: 0.6657 (m100) REVERT: B 183 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7075 (m170) REVERT: B 226 GLU cc_start: 0.7911 (mp0) cc_final: 0.7612 (mm-30) REVERT: C 21 MET cc_start: 0.3934 (tmm) cc_final: 0.3222 (tmm) REVERT: C 32 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8245 (tppp) REVERT: E 6 GLU cc_start: 0.5840 (pt0) cc_final: 0.5581 (pt0) REVERT: E 47 TRP cc_start: 0.6904 (t60) cc_final: 0.6437 (t60) REVERT: E 90 ASP cc_start: 0.5682 (m-30) cc_final: 0.5426 (m-30) outliers start: 31 outliers final: 21 residues processed: 226 average time/residue: 0.0948 time to fit residues: 29.1610 Evaluate side-chains 224 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.207067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.164196 restraints weight = 10360.412| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.45 r_work: 0.3775 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8875 Z= 0.136 Angle : 0.649 9.472 12043 Z= 0.333 Chirality : 0.044 0.248 1398 Planarity : 0.004 0.042 1505 Dihedral : 5.033 24.549 1224 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.57 % Allowed : 19.03 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1113 helix: 1.61 (0.27), residues: 344 sheet: -0.76 (0.33), residues: 256 loop : -1.05 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.016 0.001 TYR R 242 PHE 0.034 0.002 PHE R 439 TRP 0.010 0.001 TRP B 332 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8871) covalent geometry : angle 0.64825 (12035) SS BOND : bond 0.00530 ( 4) SS BOND : angle 1.46814 ( 8) hydrogen bonds : bond 0.03701 ( 394) hydrogen bonds : angle 4.88884 ( 1131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.312 Fit side-chains REVERT: A 247 MET cc_start: 0.7641 (mmp) cc_final: 0.7130 (mmp) REVERT: A 333 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7769 (tp40) REVERT: A 337 ASP cc_start: 0.7871 (m-30) cc_final: 0.7242 (m-30) REVERT: A 341 ASP cc_start: 0.8129 (m-30) cc_final: 0.7811 (m-30) REVERT: R 183 MET cc_start: 0.4975 (mmt) cc_final: 0.4748 (mmt) REVERT: R 214 MET cc_start: 0.7532 (ttm) cc_final: 0.7274 (ttm) REVERT: R 354 ARG cc_start: 0.7735 (tpp80) cc_final: 0.6218 (tpt90) REVERT: B 82 TRP cc_start: 0.7215 (m100) cc_final: 0.6659 (m100) REVERT: B 219 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7739 (ttt90) REVERT: B 226 GLU cc_start: 0.7906 (mp0) cc_final: 0.7690 (mm-30) REVERT: C 21 MET cc_start: 0.4116 (tmm) cc_final: 0.3390 (tmm) REVERT: C 32 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8322 (tppp) REVERT: E 47 TRP cc_start: 0.6926 (t60) cc_final: 0.6446 (t60) REVERT: E 90 ASP cc_start: 0.5667 (m-30) cc_final: 0.5465 (m-30) outliers start: 33 outliers final: 24 residues processed: 224 average time/residue: 0.0956 time to fit residues: 29.2445 Evaluate side-chains 226 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 0.0020 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 chunk 86 optimal weight: 0.1980 chunk 77 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.212897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170493 restraints weight = 10304.230| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.47 r_work: 0.3846 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8875 Z= 0.111 Angle : 0.636 10.653 12043 Z= 0.325 Chirality : 0.042 0.184 1398 Planarity : 0.004 0.042 1505 Dihedral : 4.779 25.231 1224 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.38 % Allowed : 20.11 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1113 helix: 1.74 (0.27), residues: 341 sheet: -0.74 (0.33), residues: 248 loop : -1.10 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.017 0.001 TYR R 242 PHE 0.034 0.001 PHE R 439 TRP 0.011 0.001 TRP B 332 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8871) covalent geometry : angle 0.63452 (12035) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.54179 ( 8) hydrogen bonds : bond 0.03432 ( 394) hydrogen bonds : angle 4.68759 ( 1131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.366 Fit side-chains REVERT: A 247 MET cc_start: 0.7521 (mmp) cc_final: 0.6961 (mmp) REVERT: A 333 GLN cc_start: 0.8251 (tp-100) cc_final: 0.8036 (tp40) REVERT: A 337 ASP cc_start: 0.7810 (m-30) cc_final: 0.7285 (m-30) REVERT: A 341 ASP cc_start: 0.8055 (m-30) cc_final: 0.7797 (m-30) REVERT: R 214 MET cc_start: 0.7486 (ttm) cc_final: 0.7205 (ttm) REVERT: R 253 MET cc_start: 0.7700 (tpp) cc_final: 0.7442 (tpp) REVERT: R 315 GLN cc_start: 0.6380 (mm-40) cc_final: 0.5496 (mp10) REVERT: R 323 TRP cc_start: 0.6795 (t-100) cc_final: 0.6564 (t-100) REVERT: B 49 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7871 (mtm-85) REVERT: B 82 TRP cc_start: 0.7023 (m100) cc_final: 0.6483 (m100) REVERT: C 21 MET cc_start: 0.4248 (tmm) cc_final: 0.3628 (tmm) REVERT: C 32 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8297 (tppp) REVERT: E 47 TRP cc_start: 0.6659 (t60) cc_final: 0.6111 (t60) REVERT: E 90 ASP cc_start: 0.5526 (m-30) cc_final: 0.5307 (m-30) outliers start: 22 outliers final: 19 residues processed: 215 average time/residue: 0.0888 time to fit residues: 26.5856 Evaluate side-chains 211 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.206164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.163403 restraints weight = 10391.286| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.45 r_work: 0.3775 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8875 Z= 0.151 Angle : 0.665 10.624 12043 Z= 0.342 Chirality : 0.044 0.293 1398 Planarity : 0.004 0.044 1505 Dihedral : 4.958 25.570 1224 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.05 % Allowed : 21.62 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1113 helix: 1.73 (0.27), residues: 341 sheet: -0.72 (0.33), residues: 253 loop : -1.06 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.018 0.002 TYR A 296 PHE 0.034 0.002 PHE R 439 TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8871) covalent geometry : angle 0.66407 (12035) SS BOND : bond 0.00536 ( 4) SS BOND : angle 1.49395 ( 8) hydrogen bonds : bond 0.03729 ( 394) hydrogen bonds : angle 4.85930 ( 1131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.329 Fit side-chains REVERT: A 247 MET cc_start: 0.7679 (mmp) cc_final: 0.7175 (mmp) REVERT: A 333 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7870 (tp40) REVERT: A 337 ASP cc_start: 0.7850 (m-30) cc_final: 0.7194 (m-30) REVERT: A 341 ASP cc_start: 0.8128 (m-30) cc_final: 0.7780 (m-30) REVERT: R 214 MET cc_start: 0.7584 (ttm) cc_final: 0.7313 (ttm) REVERT: R 223 MET cc_start: 0.7108 (tmm) cc_final: 0.6838 (tmm) REVERT: R 253 MET cc_start: 0.7890 (tpp) cc_final: 0.7071 (tpp) REVERT: R 354 ARG cc_start: 0.7625 (tpp80) cc_final: 0.6112 (tpt90) REVERT: B 49 ARG cc_start: 0.8265 (mtt90) cc_final: 0.7838 (mtm-85) REVERT: B 82 TRP cc_start: 0.7255 (m100) cc_final: 0.6740 (m100) REVERT: B 226 GLU cc_start: 0.7901 (mp0) cc_final: 0.7674 (mm-30) REVERT: C 21 MET cc_start: 0.4175 (tmm) cc_final: 0.3611 (tmm) REVERT: C 32 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8309 (tppp) REVERT: E 47 TRP cc_start: 0.6965 (t60) cc_final: 0.6488 (t60) outliers start: 19 outliers final: 18 residues processed: 207 average time/residue: 0.0869 time to fit residues: 24.9962 Evaluate side-chains 214 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.205952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163001 restraints weight = 10321.087| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.44 r_work: 0.3762 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8875 Z= 0.154 Angle : 0.673 10.935 12043 Z= 0.345 Chirality : 0.044 0.290 1398 Planarity : 0.004 0.044 1505 Dihedral : 5.018 25.827 1224 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.38 % Allowed : 21.19 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1113 helix: 1.60 (0.27), residues: 348 sheet: -0.78 (0.33), residues: 257 loop : -1.09 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.017 0.002 TYR A 296 PHE 0.035 0.002 PHE R 439 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8871) covalent geometry : angle 0.67199 (12035) SS BOND : bond 0.00545 ( 4) SS BOND : angle 1.52758 ( 8) hydrogen bonds : bond 0.03815 ( 394) hydrogen bonds : angle 4.91306 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.51 seconds wall clock time: 37 minutes 17.97 seconds (2237.97 seconds total)