Starting phenix.real_space_refine on Thu Feb 13 09:15:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yac_33708/02_2025/7yac_33708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yac_33708/02_2025/7yac_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_33708/02_2025/7yac_33708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yac_33708/02_2025/7yac_33708.map" model { file = "/net/cci-nas-00/data/ceres_data/7yac_33708/02_2025/7yac_33708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yac_33708/02_2025/7yac_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.36, per 1000 atoms: 0.60 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: 2.36 Conformation dependent library (CDL) restraints added in 974.9 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: 1.13 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: 2.76 Time building geometry restraints manager: 2.69 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: 0.850 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- 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 : 1.003 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: 0.2204 time to fit residues: 49.5470 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 : 1.022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148342 restraints weight = 11308.423| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.61 r_work: 0.3224 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 1.005 Fit side-chains REVERT: C 31 SER cc_start: 0.7310 (t) cc_final: 0.7066 (m) REVERT: E 92 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5853 (m-80) REVERT: E 153 TRP cc_start: 0.5512 (t60) cc_final: 0.5143 (t60) REVERT: E 178 MET cc_start: 0.6374 (tmm) cc_final: 0.6124 (tmm) REVERT: E 276 ASN cc_start: 0.6390 (m-40) cc_final: 0.5946 (m110) REVERT: S 195 LEU cc_start: 0.8205 (mp) cc_final: 0.7995 (mp) outliers start: 12 outliers final: 10 residues processed: 161 average time/residue: 0.2077 time to fit residues: 46.8764 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 : 0.972 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.0000 chunk 61 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.0060 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 89 optimal weight: 0.0040 chunk 75 optimal weight: 0.6980 overall best weight: 0.0510 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.191473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153334 restraints weight = 11471.547| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.76 r_work: 0.3293 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9126 Z= 0.117 Angle : 0.483 8.263 12355 Z= 0.255 Chirality : 0.040 0.142 1398 Planarity : 0.003 0.050 1550 Dihedral : 4.436 42.117 1253 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.13 % Allowed : 10.05 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.25), residues: 1126 helix: 2.38 (0.28), residues: 368 sheet: 0.28 (0.32), residues: 255 loop : -1.36 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS C 44 PHE 0.014 0.001 PHE A 189 TYR 0.009 0.001 TYR E 50 ARG 0.003 0.000 ARG S 38 *********************** 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 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.011 Fit side-chains REVERT: A 230 TYR cc_start: 0.5629 (t80) cc_final: 0.5172 (t80) REVERT: A 243 MET cc_start: 0.6324 (tmm) cc_final: 0.6094 (tmm) REVERT: C 31 SER cc_start: 0.7299 (t) cc_final: 0.7080 (m) REVERT: E 92 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.5843 (m-80) REVERT: E 178 MET cc_start: 0.6361 (tmm) cc_final: 0.6038 (tmm) REVERT: E 296 PHE cc_start: 0.6453 (t80) cc_final: 0.6140 (t80) REVERT: S 46 GLU cc_start: 0.7315 (pt0) cc_final: 0.7098 (pt0) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 0.2138 time to fit residues: 46.3016 Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL 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 78 THR 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 65 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** E 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.188711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149592 restraints weight = 11427.243| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.76 r_work: 0.3261 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1567 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= 0.137 Angle : 0.494 8.846 12355 Z= 0.260 Chirality : 0.041 0.135 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.411 39.667 1253 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.44 % Allowed : 11.79 % 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: 0.45 (0.25), residues: 1126 helix: 2.46 (0.28), residues: 367 sheet: 0.29 (0.32), residues: 269 loop : -1.45 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 153 HIS 0.002 0.001 HIS E 146 PHE 0.012 0.001 PHE A 189 TYR 0.008 0.001 TYR E 211 ARG 0.006 0.000 ARG B 219 *********************** 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 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.999 Fit side-chains REVERT: C 31 SER cc_start: 0.7342 (t) cc_final: 0.7099 (m) REVERT: E 92 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5907 (m-80) REVERT: E 178 MET cc_start: 0.6497 (tmm) cc_final: 0.6005 (tmm) REVERT: E 296 PHE cc_start: 0.6522 (t80) cc_final: 0.6189 (t80) REVERT: S 46 GLU cc_start: 0.7530 (pt0) cc_final: 0.7321 (pt0) outliers start: 14 outliers final: 11 residues processed: 149 average time/residue: 0.2207 time to fit residues: 45.1336 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 105 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN E 79 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 = 0.4117 r_free = 0.4117 target = 0.187560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148393 restraints weight = 11339.113| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.71 r_work: 0.3239 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1666 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= 0.148 Angle : 0.503 8.932 12355 Z= 0.265 Chirality : 0.041 0.136 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.460 38.181 1253 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.64 % Allowed : 13.54 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.25), residues: 1126 helix: 2.46 (0.28), residues: 366 sheet: 0.25 (0.32), residues: 269 loop : -1.44 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 153 HIS 0.002 0.001 HIS A 244 PHE 0.014 0.001 PHE A 189 TYR 0.008 0.001 TYR E 228 ARG 0.005 0.000 ARG B 219 *********************** 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 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.177 Fit side-chains REVERT: C 31 SER cc_start: 0.7327 (t) cc_final: 0.7060 (m) REVERT: C 37 LEU cc_start: 0.7536 (tp) cc_final: 0.7277 (tp) REVERT: E 92 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.5831 (m-80) REVERT: E 178 MET cc_start: 0.6441 (tmm) cc_final: 0.6161 (tmm) REVERT: E 296 PHE cc_start: 0.6541 (t80) cc_final: 0.6233 (t80) outliers start: 16 outliers final: 14 residues processed: 148 average time/residue: 0.2324 time to fit residues: 47.0379 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 : 1.030 ------------------------------------------------------------------------------- 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 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 172 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 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.0370 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.187185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145462 restraints weight = 11355.098| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.23 r_work: 0.3263 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9126 Z= 0.142 Angle : 0.499 9.070 12355 Z= 0.261 Chirality : 0.041 0.135 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.420 37.952 1253 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.44 % Allowed : 14.26 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.25), residues: 1126 helix: 2.39 (0.28), residues: 372 sheet: 0.23 (0.31), residues: 269 loop : -1.37 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR S 190 ARG 0.002 0.000 ARG E 247 *********************** 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 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.952 Fit side-chains REVERT: C 31 SER cc_start: 0.7302 (t) cc_final: 0.7012 (m) REVERT: C 37 LEU cc_start: 0.7516 (tp) cc_final: 0.7302 (tp) REVERT: E 92 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: E 178 MET cc_start: 0.6460 (tmm) cc_final: 0.6107 (tmm) outliers start: 14 outliers final: 13 residues processed: 141 average time/residue: 0.2179 time to fit residues: 42.5370 Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 172 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 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.0570 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.185402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144326 restraints weight = 11386.262| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.95 r_work: 0.3241 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9126 Z= 0.170 Angle : 0.529 9.461 12355 Z= 0.276 Chirality : 0.042 0.136 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.561 36.917 1253 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.74 % Allowed : 14.56 % Favored : 83.69 % 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: 0.43 (0.25), residues: 1126 helix: 2.38 (0.27), residues: 372 sheet: 0.10 (0.31), residues: 274 loop : -1.34 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 PHE 0.016 0.001 PHE S 177 TYR 0.024 0.001 TYR E 180 ARG 0.002 0.000 ARG S 87 *********************** 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 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.961 Fit side-chains REVERT: C 31 SER cc_start: 0.7292 (t) cc_final: 0.6997 (m) REVERT: C 37 LEU cc_start: 0.7533 (tp) cc_final: 0.7323 (tp) REVERT: E 92 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.5972 (m-80) REVERT: E 178 MET cc_start: 0.6564 (tmm) cc_final: 0.6283 (tmm) REVERT: E 296 PHE cc_start: 0.6495 (t80) cc_final: 0.6112 (t80) outliers start: 17 outliers final: 15 residues processed: 147 average time/residue: 0.2302 time to fit residues: 46.0565 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.0470 chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- 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 = 0.186459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145387 restraints weight = 11519.734| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.09 r_work: 0.3243 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1902 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= 0.157 Angle : 0.518 9.568 12355 Z= 0.270 Chirality : 0.041 0.140 1398 Planarity : 0.003 0.052 1550 Dihedral : 4.525 36.930 1253 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.54 % Allowed : 15.28 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1126 helix: 2.40 (0.28), residues: 372 sheet: 0.06 (0.31), residues: 274 loop : -1.33 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 153 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.001 PHE S 177 TYR 0.009 0.001 TYR A 287 ARG 0.003 0.000 ARG S 87 *********************** 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 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.991 Fit side-chains REVERT: E 92 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6012 (m-80) REVERT: E 178 MET cc_start: 0.6473 (tmm) cc_final: 0.6124 (tmm) REVERT: E 296 PHE cc_start: 0.6478 (t80) cc_final: 0.6097 (t80) outliers start: 15 outliers final: 14 residues processed: 147 average time/residue: 0.2117 time to fit residues: 43.0826 Evaluate side-chains 144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 305 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET 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 21 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 chunk 42 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.188037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148912 restraints weight = 11371.628| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.63 r_work: 0.3259 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2001 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= 0.135 Angle : 0.505 9.677 12355 Z= 0.262 Chirality : 0.041 0.172 1398 Planarity : 0.003 0.051 1550 Dihedral : 4.378 37.763 1253 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.54 % Allowed : 16.00 % Favored : 82.46 % 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: 0.56 (0.25), residues: 1126 helix: 2.44 (0.28), residues: 372 sheet: 0.31 (0.32), residues: 256 loop : -1.26 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 153 HIS 0.001 0.000 HIS S 167 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR S 190 ARG 0.002 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 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.064 Fit side-chains REVERT: A 21 ARG cc_start: 0.8199 (tmm-80) cc_final: 0.7958 (tmm-80) REVERT: B 304 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7604 (mmm-85) REVERT: C 37 LEU cc_start: 0.7425 (tp) cc_final: 0.7164 (tp) REVERT: E 92 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: E 178 MET cc_start: 0.6453 (tmm) cc_final: 0.6183 (tmm) outliers start: 15 outliers final: 14 residues processed: 142 average time/residue: 0.2392 time to fit residues: 45.8402 Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN E 84 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 = 0.4120 r_free = 0.4120 target = 0.187769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147036 restraints weight = 11363.520| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.03 r_work: 0.3261 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9126 Z= 0.142 Angle : 0.515 9.670 12355 Z= 0.267 Chirality : 0.041 0.195 1398 Planarity : 0.003 0.051 1550 Dihedral : 4.359 37.367 1253 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.74 % Allowed : 16.10 % Favored : 82.15 % 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: 0.54 (0.25), residues: 1126 helix: 2.43 (0.28), residues: 372 sheet: 0.30 (0.32), residues: 256 loop : -1.27 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 153 HIS 0.001 0.000 HIS B 142 PHE 0.012 0.001 PHE S 239 TYR 0.013 0.001 TYR A 230 ARG 0.001 0.000 ARG E 247 ********************** 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 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.965 Fit side-chains REVERT: A 21 ARG cc_start: 0.8148 (tmm-80) cc_final: 0.7651 (ttm170) REVERT: C 21 MET cc_start: 0.6049 (ttt) cc_final: 0.5317 (tmm) REVERT: C 37 LEU cc_start: 0.7443 (tp) cc_final: 0.7172 (tp) REVERT: E 92 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.5927 (m-80) REVERT: E 178 MET cc_start: 0.6489 (tmm) cc_final: 0.6172 (tmm) outliers start: 17 outliers final: 14 residues processed: 142 average time/residue: 0.2343 time to fit residues: 44.8373 Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 84 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 = 0.4109 r_free = 0.4109 target = 0.186698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145610 restraints weight = 11304.698| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.96 r_work: 0.3250 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9126 Z= 0.159 Angle : 0.535 9.866 12355 Z= 0.276 Chirality : 0.042 0.180 1398 Planarity : 0.003 0.053 1550 Dihedral : 4.446 36.454 1253 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.54 % Allowed : 16.41 % Favored : 82.05 % 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: 0.50 (0.25), residues: 1126 helix: 2.42 (0.28), residues: 371 sheet: 0.14 (0.31), residues: 265 loop : -1.25 (0.26), residues: 490 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 0.014 0.001 PHE S 177 TYR 0.008 0.001 TYR A 287 ARG 0.002 0.000 ARG E 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4744.29 seconds wall clock time: 84 minutes 47.88 seconds (5087.88 seconds total)