Starting phenix.real_space_refine on Tue Mar 3 21:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yac_33708/03_2026/7yac_33708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yac_33708/03_2026/7yac_33708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yac_33708/03_2026/7yac_33708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yac_33708/03_2026/7yac_33708.map" model { file = "/net/cci-nas-00/data/ceres_data/7yac_33708/03_2026/7yac_33708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yac_33708/03_2026/7yac_33708.cif" } resolution = 3.24 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= 0.001 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 5703 2.51 5 N 1508 2.21 5 O 1656 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 8937 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1817 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "E" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2218 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 269} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'IUD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.23 Number of scatterers: 8937 At special positions: 0 Unit cell: (125.8, 98.6, 123.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 F 2 9.00 O 1656 8.00 N 1508 7.00 C 5703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.57 Conformation dependent library (CDL) restraints added in 317.0 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.593A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.191A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.636A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.932A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.192A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.560A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 22 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 43 through 72 Processing helix chain 'E' and resid 76 through 104 removed outlier: 3.517A pdb=" N LEU E 91 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Proline residue: E 97 - end of helix removed outlier: 3.835A pdb=" N MET E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 102 " --> pdb=" O PHE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 146 removed outlier: 3.575A pdb=" N HIS E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 155 removed outlier: 4.200A pdb=" N TRP E 153 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 179 removed outlier: 4.172A pdb=" N MET E 161 " --> pdb=" O ARG E 157 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 200 through 217 removed outlier: 4.302A pdb=" N THR E 206 " --> pdb=" O GLY E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 242 removed outlier: 3.680A pdb=" N THR E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 282 removed outlier: 3.540A pdb=" N LYS E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 253 " --> pdb=" O LYS E 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 287 through 313 removed outlier: 3.933A pdb=" N ASN E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Proline residue: E 309 - end of helix removed outlier: 3.535A pdb=" N ALA E 313 " --> pdb=" O PRO E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 322 removed outlier: 4.214A pdb=" N LYS E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.719A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.918A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.792A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.627A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 324 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.315A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.580A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.549A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.360A 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: 6.844A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.680A 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 277 removed outlier: 6.639A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.649A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.613A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 159 removed outlier: 3.527A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS S 159 " --> pdb=" O PHE S 212 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE S 212 " --> pdb=" O CYS S 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.630A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1134 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: 1.42 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1438 1.27 - 1.41: 2313 1.41 - 1.55: 5267 1.55 - 1.68: 8 1.68 - 1.82: 100 Bond restraints: 9126 Sorted by residual: bond pdb=" C08 IUD E 401 " pdb=" N03 IUD E 401 " ideal model delta sigma weight residual 1.386 1.521 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C30 IUD E 401 " pdb=" C33 IUD E 401 " ideal model delta sigma weight residual 1.423 1.525 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C02 IUD E 401 " pdb=" N03 IUD E 401 " ideal model delta sigma weight residual 1.453 1.535 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C04 IUD E 401 " pdb=" N03 IUD E 401 " ideal model delta sigma weight residual 1.457 1.534 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C01 IUD E 401 " pdb=" C06 IUD E 401 " ideal model delta sigma weight residual 1.534 1.461 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 9121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 12162 1.97 - 3.93: 160 3.93 - 5.90: 24 5.90 - 7.87: 8 7.87 - 9.83: 1 Bond angle restraints: 12355 Sorted by residual: angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 109.06 115.44 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N ARG B 68 " pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 114.56 110.33 4.23 1.27e+00 6.20e-01 1.11e+01 angle pdb=" CB MET E 178 " pdb=" CG MET E 178 " pdb=" SD MET E 178 " ideal model delta sigma weight residual 112.70 122.53 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA MET E 178 " pdb=" CB MET E 178 " pdb=" CG MET E 178 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.69e+00 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 7.99e+00 ... (remaining 12350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4854 17.59 - 35.18: 448 35.18 - 52.76: 100 52.76 - 70.35: 14 70.35 - 87.94: 5 Dihedral angle restraints: 5421 sinusoidal: 2121 harmonic: 3300 Sorted by residual: dihedral pdb=" CA ARG E 155 " pdb=" C ARG E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASN A 269 " pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 5418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 823 0.028 - 0.055: 355 0.055 - 0.083: 132 0.083 - 0.111: 64 0.111 - 0.138: 24 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA PRO E 309 " pdb=" N PRO E 309 " pdb=" C PRO E 309 " pdb=" CB PRO E 309 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CG LEU S 166 " pdb=" CB LEU S 166 " pdb=" CD1 LEU S 166 " pdb=" CD2 LEU S 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1395 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 308 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO E 309 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 309 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO S 148 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO S 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.025 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1481 2.77 - 3.30: 8299 3.30 - 3.83: 13888 3.83 - 4.37: 15641 4.37 - 4.90: 28047 Nonbonded interactions: 67356 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.235 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A 186 " pdb=" NE2 HIS A 188 " model vdw 2.317 3.120 nonbonded pdb=" NE ARG B 137 " pdb=" O ILE B 171 " model vdw 2.322 3.120 ... (remaining 67351 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.050 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.004 0.135 9127 Z= 0.191 Angle : 0.590 9.833 12357 Z= 0.320 Chirality : 0.040 0.138 1398 Planarity : 0.004 0.057 1550 Dihedral : 14.304 87.937 3292 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.25), residues: 1126 helix: 1.68 (0.27), residues: 370 sheet: 0.15 (0.32), residues: 271 loop : -1.33 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 38 TYR 0.014 0.001 TYR E 50 PHE 0.011 0.001 PHE S 177 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9126) covalent geometry : angle 0.58986 (12355) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.68276 ( 2) hydrogen bonds : bond 0.19667 ( 399) hydrogen bonds : angle 6.01899 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.293 Fit side-chains REVERT: C 21 MET cc_start: 0.5655 (ttt) cc_final: 0.5200 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0888 time to fit residues: 20.0578 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN E 276 ASN E 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145449 restraints weight = 11439.215| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.94 r_work: 0.3234 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9127 Z= 0.130 Angle : 0.568 9.139 12357 Z= 0.300 Chirality : 0.043 0.139 1398 Planarity : 0.004 0.052 1550 Dihedral : 4.882 40.352 1253 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.23 % Allowed : 6.87 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1126 helix: 2.13 (0.27), residues: 368 sheet: 0.10 (0.32), residues: 276 loop : -1.39 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 247 TYR 0.010 0.001 TYR S 190 PHE 0.018 0.001 PHE S 177 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9126) covalent geometry : angle 0.56777 (12355) SS BOND : bond 0.00610 ( 1) SS BOND : angle 1.46578 ( 2) hydrogen bonds : bond 0.04968 ( 399) hydrogen bonds : angle 4.44676 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.326 Fit side-chains REVERT: C 31 SER cc_start: 0.7291 (t) cc_final: 0.7033 (m) REVERT: E 92 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5810 (m-80) REVERT: E 178 MET cc_start: 0.6367 (tmm) cc_final: 0.6115 (tmm) REVERT: E 276 ASN cc_start: 0.6413 (m-40) cc_final: 0.5989 (m110) REVERT: S 78 THR cc_start: 0.7505 (p) cc_final: 0.7286 (p) REVERT: S 195 LEU cc_start: 0.8205 (mp) cc_final: 0.7996 (mp) outliers start: 12 outliers final: 10 residues processed: 161 average time/residue: 0.0824 time to fit residues: 18.9025 Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 90 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.187389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132565 restraints weight = 11401.018| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.84 r_work: 0.3312 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9127 Z= 0.101 Angle : 0.515 8.645 12357 Z= 0.272 Chirality : 0.041 0.141 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.638 40.548 1253 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.23 % Allowed : 10.15 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.25), residues: 1126 helix: 2.28 (0.27), residues: 368 sheet: 0.21 (0.32), residues: 263 loop : -1.44 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 38 TYR 0.009 0.001 TYR E 50 PHE 0.015 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9126) covalent geometry : angle 0.51463 (12355) SS BOND : bond 0.00515 ( 1) SS BOND : angle 0.92371 ( 2) hydrogen bonds : bond 0.04087 ( 399) hydrogen bonds : angle 4.16589 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.335 Fit side-chains REVERT: C 31 SER cc_start: 0.7253 (t) cc_final: 0.7000 (m) REVERT: E 92 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5677 (m-80) REVERT: E 178 MET cc_start: 0.6380 (tmm) cc_final: 0.6013 (tmm) REVERT: S 76 LYS cc_start: 0.7214 (mtmm) cc_final: 0.6938 (mmtm) outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 0.0970 time to fit residues: 19.5998 Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145743 restraints weight = 11491.942| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.01 r_work: 0.3232 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9127 Z= 0.109 Angle : 0.520 8.881 12357 Z= 0.275 Chirality : 0.042 0.136 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.634 39.260 1253 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.74 % Allowed : 12.72 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.25), residues: 1126 helix: 2.32 (0.27), residues: 367 sheet: 0.21 (0.32), residues: 269 loop : -1.57 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.008 0.001 TYR E 228 PHE 0.015 0.001 PHE S 177 TRP 0.012 0.001 TRP E 153 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9126) covalent geometry : angle 0.52018 (12355) SS BOND : bond 0.00529 ( 1) SS BOND : angle 1.09237 ( 2) hydrogen bonds : bond 0.04079 ( 399) hydrogen bonds : angle 4.03609 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.338 Fit side-chains REVERT: C 31 SER cc_start: 0.7287 (t) cc_final: 0.7011 (m) REVERT: E 92 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.5856 (m-80) REVERT: E 178 MET cc_start: 0.6510 (tmm) cc_final: 0.5971 (tmm) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.0951 time to fit residues: 19.6610 Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142075 restraints weight = 11467.684| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.78 r_work: 0.3182 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9127 Z= 0.140 Angle : 0.568 9.367 12357 Z= 0.300 Chirality : 0.043 0.137 1398 Planarity : 0.004 0.056 1550 Dihedral : 4.884 37.096 1253 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.36 % Allowed : 14.26 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.25), residues: 1126 helix: 2.10 (0.27), residues: 370 sheet: -0.02 (0.31), residues: 273 loop : -1.52 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 247 TYR 0.009 0.002 TYR S 94 PHE 0.022 0.002 PHE S 177 TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9126) covalent geometry : angle 0.56820 (12355) SS BOND : bond 0.00675 ( 1) SS BOND : angle 1.47680 ( 2) hydrogen bonds : bond 0.04685 ( 399) hydrogen bonds : angle 4.09603 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.317 Fit side-chains REVERT: A 243 MET cc_start: 0.6467 (tmm) cc_final: 0.6236 (tmm) REVERT: C 21 MET cc_start: 0.6155 (ttt) cc_final: 0.5367 (tmm) REVERT: C 31 SER cc_start: 0.7336 (t) cc_final: 0.7048 (m) REVERT: E 92 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: E 178 MET cc_start: 0.6440 (tmm) cc_final: 0.6112 (tmm) outliers start: 23 outliers final: 19 residues processed: 148 average time/residue: 0.0954 time to fit residues: 19.3736 Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 0.0050 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.184050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143393 restraints weight = 11371.184| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.85 r_work: 0.3204 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9127 Z= 0.125 Angle : 0.543 9.227 12357 Z= 0.287 Chirality : 0.042 0.137 1398 Planarity : 0.004 0.054 1550 Dihedral : 4.851 37.819 1253 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.15 % Allowed : 15.18 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.25), residues: 1126 helix: 2.09 (0.27), residues: 370 sheet: -0.01 (0.31), residues: 273 loop : -1.52 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 247 TYR 0.008 0.001 TYR S 190 PHE 0.020 0.001 PHE S 177 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9126) covalent geometry : angle 0.54242 (12355) SS BOND : bond 0.00640 ( 1) SS BOND : angle 1.30134 ( 2) hydrogen bonds : bond 0.04407 ( 399) hydrogen bonds : angle 4.05630 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.303 Fit side-chains REVERT: A 243 MET cc_start: 0.6400 (tmm) cc_final: 0.6179 (tmm) REVERT: C 21 MET cc_start: 0.6089 (ttt) cc_final: 0.5319 (tmm) REVERT: C 31 SER cc_start: 0.7369 (t) cc_final: 0.7044 (m) REVERT: E 92 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: E 178 MET cc_start: 0.6433 (tmm) cc_final: 0.6071 (tmm) outliers start: 21 outliers final: 18 residues processed: 147 average time/residue: 0.0879 time to fit residues: 17.9795 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.185586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144764 restraints weight = 11418.522| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.78 r_work: 0.3234 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9127 Z= 0.102 Angle : 0.514 9.366 12357 Z= 0.270 Chirality : 0.041 0.139 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.668 38.598 1253 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.85 % Allowed : 15.79 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.25), residues: 1126 helix: 2.21 (0.27), residues: 370 sheet: -0.00 (0.31), residues: 274 loop : -1.39 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 247 TYR 0.016 0.001 TYR E 180 PHE 0.015 0.001 PHE S 177 TRP 0.014 0.001 TRP E 153 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9126) covalent geometry : angle 0.51398 (12355) SS BOND : bond 0.00515 ( 1) SS BOND : angle 0.99113 ( 2) hydrogen bonds : bond 0.03898 ( 399) hydrogen bonds : angle 3.95692 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.318 Fit side-chains REVERT: C 21 MET cc_start: 0.6088 (ttt) cc_final: 0.5361 (tmm) REVERT: C 31 SER cc_start: 0.7288 (t) cc_final: 0.6953 (m) REVERT: E 92 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: E 178 MET cc_start: 0.6693 (tmm) cc_final: 0.6410 (tmm) outliers start: 18 outliers final: 16 residues processed: 147 average time/residue: 0.0907 time to fit residues: 18.4591 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.0070 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145298 restraints weight = 11319.187| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.61 r_work: 0.3205 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9127 Z= 0.114 Angle : 0.536 9.443 12357 Z= 0.281 Chirality : 0.042 0.140 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.687 37.886 1253 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.15 % Allowed : 16.62 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.25), residues: 1126 helix: 2.18 (0.27), residues: 370 sheet: -0.04 (0.31), residues: 274 loop : -1.42 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 247 TYR 0.008 0.001 TYR S 190 PHE 0.017 0.001 PHE S 177 TRP 0.014 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9126) covalent geometry : angle 0.53602 (12355) SS BOND : bond 0.00589 ( 1) SS BOND : angle 1.17125 ( 2) hydrogen bonds : bond 0.04101 ( 399) hydrogen bonds : angle 3.95482 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.320 Fit side-chains REVERT: B 267 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6693 (t0) REVERT: C 21 MET cc_start: 0.6122 (ttt) cc_final: 0.5361 (tmm) REVERT: E 92 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: E 178 MET cc_start: 0.6404 (tmm) cc_final: 0.6107 (tmm) outliers start: 21 outliers final: 19 residues processed: 143 average time/residue: 0.0893 time to fit residues: 17.7243 Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 0.3980 chunk 65 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.183515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142361 restraints weight = 11373.111| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.88 r_work: 0.3193 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9127 Z= 0.134 Angle : 0.573 9.814 12357 Z= 0.298 Chirality : 0.043 0.166 1398 Planarity : 0.004 0.056 1550 Dihedral : 4.853 36.581 1253 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.26 % Allowed : 16.82 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.25), residues: 1126 helix: 2.08 (0.27), residues: 370 sheet: -0.02 (0.31), residues: 272 loop : -1.46 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 247 TYR 0.011 0.001 TYR A 287 PHE 0.020 0.001 PHE S 177 TRP 0.014 0.001 TRP E 153 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9126) covalent geometry : angle 0.57289 (12355) SS BOND : bond 0.00681 ( 1) SS BOND : angle 1.41661 ( 2) hydrogen bonds : bond 0.04530 ( 399) hydrogen bonds : angle 4.03352 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.333 Fit side-chains REVERT: B 267 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6737 (t0) REVERT: C 21 MET cc_start: 0.6035 (ttt) cc_final: 0.5288 (tmm) REVERT: E 74 MET cc_start: 0.4124 (mmm) cc_final: 0.3481 (mmp) REVERT: E 92 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: E 178 MET cc_start: 0.6502 (tmm) cc_final: 0.6160 (tmm) outliers start: 22 outliers final: 20 residues processed: 144 average time/residue: 0.0856 time to fit residues: 17.2139 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 HIS ** 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 = 0.4094 r_free = 0.4094 target = 0.185430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131385 restraints weight = 11313.418| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.86 r_work: 0.3257 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9127 Z= 0.106 Angle : 0.533 9.688 12357 Z= 0.276 Chirality : 0.042 0.185 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.660 38.187 1253 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.15 % Allowed : 17.03 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.25), residues: 1126 helix: 2.20 (0.27), residues: 370 sheet: -0.12 (0.30), residues: 284 loop : -1.37 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 87 TYR 0.009 0.001 TYR A 287 PHE 0.016 0.001 PHE S 177 TRP 0.016 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9126) covalent geometry : angle 0.53247 (12355) SS BOND : bond 0.00533 ( 1) SS BOND : angle 1.06002 ( 2) hydrogen bonds : bond 0.03936 ( 399) hydrogen bonds : angle 3.94644 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.327 Fit side-chains REVERT: B 267 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6670 (t0) REVERT: B 304 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7684 (mmm-85) REVERT: C 21 MET cc_start: 0.5987 (ttt) cc_final: 0.5294 (tmm) REVERT: E 92 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: E 178 MET cc_start: 0.6417 (tmm) cc_final: 0.6041 (tmm) outliers start: 21 outliers final: 19 residues processed: 150 average time/residue: 0.0939 time to fit residues: 19.4241 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 340 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.184752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142982 restraints weight = 11246.134| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.92 r_work: 0.3194 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9127 Z= 0.119 Angle : 0.555 9.699 12357 Z= 0.290 Chirality : 0.042 0.168 1398 Planarity : 0.004 0.054 1550 Dihedral : 4.698 37.458 1253 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.36 % Allowed : 17.33 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.25), residues: 1126 helix: 2.18 (0.27), residues: 370 sheet: -0.12 (0.31), residues: 274 loop : -1.39 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.009 0.001 TYR A 287 PHE 0.019 0.001 PHE S 177 TRP 0.016 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9126) covalent geometry : angle 0.55533 (12355) SS BOND : bond 0.00605 ( 1) SS BOND : angle 1.21313 ( 2) hydrogen bonds : bond 0.04131 ( 399) hydrogen bonds : angle 3.95910 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.72 seconds wall clock time: 40 minutes 37.25 seconds (2437.25 seconds total)