Starting phenix.real_space_refine on Sat Dec 28 17:22:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yac_33708/12_2024/7yac_33708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yac_33708/12_2024/7yac_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_33708/12_2024/7yac_33708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yac_33708/12_2024/7yac_33708.map" model { file = "/net/cci-nas-00/data/ceres_data/7yac_33708/12_2024/7yac_33708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yac_33708/12_2024/7yac_33708.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.94, per 1000 atoms: 0.66 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.50 Time building geometry restraints manager: 2.57 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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 9126 Z= 0.271 Angle : 0.590 9.833 12355 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (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 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE S 177 TYR 0.014 0.001 TYR E 50 ARG 0.003 0.000 ARG S 38 *********************** 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 : 1.023 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: 0.2365 time to fit residues: 53.6601 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 : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9126 Z= 0.179 Angle : 0.567 9.115 12355 Z= 0.299 Chirality : 0.043 0.138 1398 Planarity : 0.004 0.053 1550 Dihedral : 4.874 39.671 1253 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.23 % Allowed : 6.67 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1126 helix: 2.14 (0.27), residues: 368 sheet: 0.11 (0.32), residues: 269 loop : -1.42 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.001 PHE S 177 TYR 0.010 0.001 TYR E 50 ARG 0.002 0.000 ARG E 247 *********************** 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 : 0.969 Fit side-chains REVERT: C 31 SER cc_start: 0.7389 (t) cc_final: 0.7179 (m) REVERT: E 92 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: E 153 TRP cc_start: 0.5183 (t60) cc_final: 0.4801 (t60) REVERT: E 178 MET cc_start: 0.6318 (tmm) cc_final: 0.6090 (tmm) REVERT: E 276 ASN cc_start: 0.6382 (m-40) cc_final: 0.6024 (m110) REVERT: S 195 LEU cc_start: 0.8098 (mp) cc_final: 0.7866 (mp) outliers start: 12 outliers final: 10 residues processed: 161 average time/residue: 0.2074 time to fit residues: 47.3122 Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9126 Z= 0.213 Angle : 0.578 9.123 12355 Z= 0.306 Chirality : 0.043 0.141 1398 Planarity : 0.004 0.055 1550 Dihedral : 4.977 38.521 1253 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.26 % Allowed : 10.97 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1126 helix: 2.09 (0.27), residues: 367 sheet: 0.01 (0.31), residues: 279 loop : -1.62 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.023 0.002 PHE S 177 TYR 0.011 0.002 TYR S 94 ARG 0.003 0.000 ARG S 98 *********************** 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 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.063 Fit side-chains REVERT: A 243 MET cc_start: 0.5965 (tmm) cc_final: 0.5662 (tmm) REVERT: C 21 MET cc_start: 0.6138 (ttt) cc_final: 0.5492 (tmm) REVERT: C 31 SER cc_start: 0.7389 (t) cc_final: 0.7146 (m) REVERT: E 92 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.5911 (m-80) REVERT: E 153 TRP cc_start: 0.5210 (t60) cc_final: 0.4895 (t60) REVERT: E 178 MET cc_start: 0.6399 (tmm) cc_final: 0.5983 (tmm) outliers start: 22 outliers final: 17 residues processed: 147 average time/residue: 0.2305 time to fit residues: 46.4071 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 47 THR 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 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 Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9126 Z= 0.150 Angle : 0.517 8.635 12355 Z= 0.274 Chirality : 0.041 0.141 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.736 39.464 1253 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 14.15 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1126 helix: 2.28 (0.27), residues: 366 sheet: 0.08 (0.31), residues: 273 loop : -1.57 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.017 0.001 PHE S 177 TYR 0.007 0.001 TYR E 50 ARG 0.002 0.000 ARG E 154 *********************** 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 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.925 Fit side-chains REVERT: C 21 MET cc_start: 0.6083 (ttt) cc_final: 0.5496 (tmm) REVERT: C 31 SER cc_start: 0.7397 (t) cc_final: 0.7150 (m) REVERT: E 92 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6062 (m-80) REVERT: E 178 MET cc_start: 0.6493 (tmm) cc_final: 0.5980 (tmm) outliers start: 14 outliers final: 12 residues processed: 145 average time/residue: 0.2245 time to fit residues: 44.7075 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET 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 255 LEU Chi-restraints excluded: chain B residue 269 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9126 Z= 0.267 Angle : 0.617 9.558 12355 Z= 0.326 Chirality : 0.044 0.158 1398 Planarity : 0.004 0.060 1550 Dihedral : 5.202 36.315 1253 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 2.46 % Allowed : 14.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1126 helix: 1.95 (0.27), residues: 369 sheet: -0.19 (0.31), residues: 275 loop : -1.58 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.027 0.002 PHE S 177 TYR 0.012 0.002 TYR S 94 ARG 0.003 0.000 ARG E 247 *********************** 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 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.076 Fit side-chains REVERT: B 267 ASP cc_start: 0.6078 (OUTLIER) cc_final: 0.5764 (t0) REVERT: C 21 MET cc_start: 0.6085 (ttt) cc_final: 0.5431 (tmm) REVERT: E 92 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: E 178 MET cc_start: 0.6346 (tmm) cc_final: 0.5964 (tmm) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.2676 time to fit residues: 54.3483 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 : 1.084 ------------------------------------------------------------------------------- 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 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 47 THR 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 300 LEU 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 98 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.0470 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9126 Z= 0.138 Angle : 0.508 8.735 12355 Z= 0.268 Chirality : 0.041 0.144 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.713 39.426 1253 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.05 % Allowed : 16.62 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1126 helix: 2.26 (0.28), residues: 366 sheet: -0.02 (0.31), residues: 274 loop : -1.53 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.014 0.001 PHE S 177 TYR 0.007 0.001 TYR S 102 ARG 0.002 0.000 ARG S 72 *********************** 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 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.070 Fit side-chains REVERT: C 21 MET cc_start: 0.6060 (ttt) cc_final: 0.5480 (tmm) REVERT: E 92 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: E 178 MET cc_start: 0.6212 (tmm) cc_final: 0.5912 (tmm) REVERT: S 192 MET cc_start: 0.8680 (ppp) cc_final: 0.8170 (ptm) outliers start: 20 outliers final: 16 residues processed: 148 average time/residue: 0.2279 time to fit residues: 46.3156 Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain B residue 135 VAL 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 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 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9126 Z= 0.164 Angle : 0.534 9.311 12355 Z= 0.280 Chirality : 0.042 0.140 1398 Planarity : 0.004 0.054 1550 Dihedral : 4.704 38.723 1253 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.26 % Allowed : 16.72 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1126 helix: 2.28 (0.27), residues: 364 sheet: 0.06 (0.31), residues: 270 loop : -1.49 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.001 PHE S 177 TYR 0.021 0.001 TYR E 180 ARG 0.003 0.000 ARG E 256 *********************** 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 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.959 Fit side-chains REVERT: C 21 MET cc_start: 0.6108 (ttt) cc_final: 0.5492 (tmm) REVERT: E 92 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: E 178 MET cc_start: 0.6386 (tmm) cc_final: 0.6100 (tmm) REVERT: S 192 MET cc_start: 0.8730 (ppp) cc_final: 0.8223 (ptm) outliers start: 22 outliers final: 19 residues processed: 148 average time/residue: 0.2255 time to fit residues: 46.1040 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 37 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.0170 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9126 Z= 0.208 Angle : 0.572 9.673 12355 Z= 0.300 Chirality : 0.043 0.147 1398 Planarity : 0.004 0.056 1550 Dihedral : 4.893 36.861 1253 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1126 helix: 2.05 (0.27), residues: 370 sheet: 0.01 (0.31), residues: 272 loop : -1.52 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.019 0.002 PHE S 177 TYR 0.009 0.001 TYR S 94 ARG 0.003 0.000 ARG E 247 *********************** 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 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.025 Fit side-chains REVERT: C 21 MET cc_start: 0.6098 (ttt) cc_final: 0.5473 (tmm) REVERT: E 74 MET cc_start: 0.3874 (mmm) cc_final: 0.3517 (mmt) REVERT: E 92 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: E 178 MET cc_start: 0.6254 (tmm) cc_final: 0.5932 (tmm) REVERT: S 192 MET cc_start: 0.8728 (ppp) cc_final: 0.8340 (ptm) outliers start: 25 outliers final: 21 residues processed: 151 average time/residue: 0.2316 time to fit residues: 47.8867 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 : 0.980 ------------------------------------------------------------------------------- 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 37 ILE 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 135 VAL Chi-restraints excluded: chain E residue 150 SER 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 222 GLU 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 101 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 0.0070 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9126 Z= 0.213 Angle : 0.586 9.893 12355 Z= 0.306 Chirality : 0.043 0.171 1398 Planarity : 0.004 0.056 1550 Dihedral : 4.965 37.457 1253 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1126 helix: 1.96 (0.27), residues: 370 sheet: -0.13 (0.30), residues: 282 loop : -1.55 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 153 HIS 0.002 0.001 HIS B 142 PHE 0.023 0.002 PHE S 177 TYR 0.010 0.001 TYR A 287 ARG 0.003 0.000 ARG S 87 *********************** 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 157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.032 Fit side-chains REVERT: C 21 MET cc_start: 0.6060 (ttt) cc_final: 0.5438 (tmm) REVERT: E 74 MET cc_start: 0.4086 (mmm) cc_final: 0.3472 (mmp) REVERT: E 92 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: E 178 MET cc_start: 0.6270 (tmm) cc_final: 0.5937 (tmm) REVERT: S 192 MET cc_start: 0.8697 (ppp) cc_final: 0.8390 (ptm) outliers start: 25 outliers final: 21 residues processed: 149 average time/residue: 0.2269 time to fit residues: 46.2566 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 37 ILE 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 135 VAL Chi-restraints excluded: chain E residue 150 SER 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 222 GLU 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 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 0.0170 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9126 Z= 0.158 Angle : 0.544 9.910 12355 Z= 0.283 Chirality : 0.042 0.164 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.734 38.553 1253 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.15 % Allowed : 18.15 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1126 helix: 2.10 (0.28), residues: 370 sheet: -0.06 (0.30), residues: 280 loop : -1.47 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE S 177 TYR 0.010 0.001 TYR A 287 ARG 0.002 0.000 ARG E 256 ********************** 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 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.946 Fit side-chains REVERT: B 251 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8230 (mtt90) REVERT: B 304 ARG cc_start: 0.7692 (mtp180) cc_final: 0.7468 (mmm-85) REVERT: C 21 MET cc_start: 0.6066 (ttt) cc_final: 0.5468 (tmm) REVERT: E 74 MET cc_start: 0.4057 (mmm) cc_final: 0.3432 (mmp) REVERT: E 92 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: E 178 MET cc_start: 0.6244 (tmm) cc_final: 0.5898 (tmm) REVERT: S 83 MET cc_start: 0.5490 (mtm) cc_final: 0.5180 (mtt) REVERT: S 192 MET cc_start: 0.8680 (ppp) cc_final: 0.8327 (ptm) outliers start: 21 outliers final: 20 residues processed: 149 average time/residue: 0.2397 time to fit residues: 47.9985 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 37 ILE 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 135 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 300 LEU 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 222 GLU 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 82 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.183416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141366 restraints weight = 11263.414| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.91 r_work: 0.3190 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9126 Z= 0.217 Angle : 0.587 9.887 12355 Z= 0.306 Chirality : 0.043 0.172 1398 Planarity : 0.004 0.057 1550 Dihedral : 4.933 36.845 1253 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.26 % Allowed : 17.64 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1126 helix: 2.02 (0.27), residues: 370 sheet: -0.14 (0.30), residues: 286 loop : -1.49 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 153 HIS 0.003 0.001 HIS S 35 PHE 0.025 0.002 PHE S 177 TYR 0.012 0.002 TYR A 287 ARG 0.005 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.36 seconds wall clock time: 38 minutes 29.31 seconds (2309.31 seconds total)