Starting phenix.real_space_refine on Sat Aug 23 02:47:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz2_37944/08_2025/8wz2_37944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz2_37944/08_2025/8wz2_37944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz2_37944/08_2025/8wz2_37944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz2_37944/08_2025/8wz2_37944.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz2_37944/08_2025/8wz2_37944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz2_37944/08_2025/8wz2_37944.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5956 2.51 5 N 1605 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9355 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "L" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 147 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Time building chain proxies: 1.75, per 1000 atoms: 0.19 Number of scatterers: 9355 At special positions: 0 Unit cell: (115.34, 147.46, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1729 8.00 N 1605 7.00 C 5956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 201 " distance=1.89 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 247.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 40.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.663A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.575A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.141A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.813A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.246A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.858A pdb=" N ARG A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.729A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.679A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.616A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.701A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.853A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'L' and resid 99 through 111 Processing helix chain 'R' and resid 10 through 19 removed outlier: 3.933A pdb=" N HIS R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 30 Processing helix chain 'R' and resid 41 through 72 Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 108 removed outlier: 3.733A pdb=" N ILE R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 83 " --> pdb=" O VAL R 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 116 through 149 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 149 through 157 removed outlier: 4.067A pdb=" N TRP R 155 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 183 Proline residue: R 179 - end of helix removed outlier: 3.838A pdb=" N HIS R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.992A pdb=" N GLN R 211 " --> pdb=" O SER R 207 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS R 212 " --> pdb=" O PRO R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 Processing helix chain 'R' and resid 262 through 298 removed outlier: 3.759A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.591A pdb=" N GLU R 297 " --> pdb=" O HIS R 293 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR R 298 " --> pdb=" O MET R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.717A pdb=" N TYR R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 323 Processing helix chain 'R' and resid 323 through 334 removed outlier: 3.657A pdb=" N CYS R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 344 removed outlier: 3.930A pdb=" N LEU R 344 " --> pdb=" O LYS R 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.105A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.867A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.554A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.662A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.694A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.965A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.470A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.309A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 7.130A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.713A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.713A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 184 through 191 removed outlier: 3.622A pdb=" N LEU R 202 " --> pdb=" O GLN R 185 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS R 196 " --> pdb=" O ASP R 191 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.88 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: 1519 1.27 - 1.41: 2399 1.41 - 1.54: 5462 1.54 - 1.68: 67 1.68 - 1.81: 99 Bond restraints: 9546 Sorted by residual: bond pdb=" C GLU R 203 " pdb=" N GLU R 204 " ideal model delta sigma weight residual 1.331 1.578 -0.248 1.48e-02 4.57e+03 2.81e+02 bond pdb=" C ALA R 27 " pdb=" O ALA R 27 " ideal model delta sigma weight residual 1.236 1.136 0.100 1.15e-02 7.56e+03 7.62e+01 bond pdb=" C GLU R 23 " pdb=" O GLU R 23 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.26e-02 6.30e+03 2.76e+01 bond pdb=" CA THR R 37 " pdb=" C THR R 37 " ideal model delta sigma weight residual 1.528 1.469 0.059 1.18e-02 7.18e+03 2.51e+01 bond pdb=" CA ARG R 22 " pdb=" C ARG R 22 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.37e-02 5.33e+03 1.63e+01 ... (remaining 9541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 12803 2.23 - 4.45: 92 4.45 - 6.68: 20 6.68 - 8.91: 4 8.91 - 11.13: 12 Bond angle restraints: 12931 Sorted by residual: angle pdb=" O ILE R 199 " pdb=" C ILE R 199 " pdb=" N CYS R 200 " ideal model delta sigma weight residual 122.45 112.32 10.13 1.07e+00 8.73e-01 8.95e+01 angle pdb=" C ILE R 199 " pdb=" N CYS R 200 " pdb=" CA CYS R 200 " ideal model delta sigma weight residual 123.00 133.83 -10.83 1.38e+00 5.25e-01 6.16e+01 angle pdb=" N THR R 37 " pdb=" CA THR R 37 " pdb=" C THR R 37 " ideal model delta sigma weight residual 110.08 99.53 10.55 1.38e+00 5.25e-01 5.84e+01 angle pdb=" N ILE R 26 " pdb=" CA ILE R 26 " pdb=" C ILE R 26 " ideal model delta sigma weight residual 110.62 103.17 7.45 1.02e+00 9.61e-01 5.34e+01 angle pdb=" CA ILE R 199 " pdb=" C ILE R 199 " pdb=" N CYS R 200 " ideal model delta sigma weight residual 116.59 126.91 -10.32 1.44e+00 4.82e-01 5.13e+01 ... (remaining 12926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5562 17.98 - 35.96: 91 35.96 - 53.94: 19 53.94 - 71.93: 4 71.93 - 89.91: 1 Dihedral angle restraints: 5677 sinusoidal: 2189 harmonic: 3488 Sorted by residual: dihedral pdb=" N GLN R 24 " pdb=" C GLN R 24 " pdb=" CA GLN R 24 " pdb=" CB GLN R 24 " ideal model delta harmonic sigma weight residual 122.80 132.29 -9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C GLN R 24 " pdb=" N GLN R 24 " pdb=" CA GLN R 24 " pdb=" CB GLN R 24 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU R 39 " pdb=" CG GLU R 39 " pdb=" CD GLU R 39 " pdb=" OE1 GLU R 39 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 1468 0.340 - 0.679: 0 0.679 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.698: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CG LEU R 54 " pdb=" CB LEU R 54 " pdb=" CD1 LEU R 54 " pdb=" CD2 LEU R 54 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" CB VAL R 79 " pdb=" CA VAL R 79 " pdb=" CG1 VAL R 79 " pdb=" CG2 VAL R 79 " both_signs ideal model delta sigma weight residual False -2.63 -1.12 -1.50 2.00e-01 2.50e+01 5.66e+01 chirality pdb=" CB VAL R 279 " pdb=" CA VAL R 279 " pdb=" CG1 VAL R 279 " pdb=" CG2 VAL R 279 " both_signs ideal model delta sigma weight residual False -2.63 -1.14 -1.49 2.00e-01 2.50e+01 5.56e+01 ... (remaining 1468 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 21 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C THR R 21 " -0.061 2.00e-02 2.50e+03 pdb=" O THR R 21 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG R 22 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 29 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C TYR R 29 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR R 29 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 30 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 183 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C VAL R 183 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL R 183 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN R 184 " -0.013 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 102 2.60 - 3.18: 8324 3.18 - 3.75: 14214 3.75 - 4.33: 20031 4.33 - 4.90: 33654 Nonbonded interactions: 76325 Sorted by model distance: nonbonded pdb=" O MET R 295 " pdb=" OG SER R 299 " model vdw 2.029 3.040 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.044 3.040 nonbonded pdb=" OH TYR R 190 " pdb=" OE1 GLU R 195 " model vdw 2.125 3.040 nonbonded pdb=" OG SER R 73 " pdb=" OD1 ASN R 342 " model vdw 2.134 3.040 nonbonded pdb=" O SER A 242 " pdb=" ND2 ASN A 246 " model vdw 2.137 3.120 ... (remaining 76320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.820 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 0.248 9547 Z= 0.289 Angle : 0.584 11.132 12933 Z= 0.365 Chirality : 0.082 1.698 1471 Planarity : 0.002 0.035 1638 Dihedral : 7.423 89.908 3418 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.23), residues: 1181 helix: 0.54 (0.24), residues: 420 sheet: -0.61 (0.30), residues: 265 loop : -1.76 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 121 TYR 0.024 0.001 TYR R 36 PHE 0.021 0.001 PHE B 239 TRP 0.005 0.001 TRP R 181 HIS 0.012 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9546) covalent geometry : angle 0.58008 (12931) SS BOND : bond 0.14249 ( 1) SS BOND : angle 5.48933 ( 2) hydrogen bonds : bond 0.18406 ( 465) hydrogen bonds : angle 6.49432 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 ASN cc_start: 0.7658 (m-40) cc_final: 0.7291 (m-40) REVERT: B 251 ASP cc_start: 0.7324 (p0) cc_final: 0.7118 (p0) REVERT: R 207 SER cc_start: 0.7551 (t) cc_final: 0.6633 (t) outliers start: 1 outliers final: 2 residues processed: 410 average time/residue: 0.5459 time to fit residues: 237.0250 Evaluate side-chains 223 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 23 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 300 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 167 HIS E 194 ASN R 106 ASN R 125 GLN R 290 HIS R 338 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.071265 restraints weight = 20992.280| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.60 r_work: 0.2928 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9547 Z= 0.196 Angle : 0.681 8.247 12933 Z= 0.350 Chirality : 0.045 0.163 1471 Planarity : 0.005 0.071 1638 Dihedral : 4.625 91.152 1300 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.30 % Allowed : 17.28 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.24), residues: 1181 helix: 1.42 (0.24), residues: 427 sheet: -0.16 (0.31), residues: 267 loop : -1.33 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 356 TYR 0.016 0.002 TYR R 68 PHE 0.015 0.002 PHE R 217 TRP 0.013 0.002 TRP E 46 HIS 0.009 0.002 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9546) covalent geometry : angle 0.68080 (12931) SS BOND : bond 0.00556 ( 1) SS BOND : angle 1.11848 ( 2) hydrogen bonds : bond 0.03766 ( 465) hydrogen bonds : angle 4.74870 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8300 (tp40) REVERT: A 185 PHE cc_start: 0.6841 (m-80) cc_final: 0.6518 (m-10) REVERT: B 28 LYS cc_start: 0.8950 (tmmm) cc_final: 0.8733 (ttmm) REVERT: B 177 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8635 (mm-30) REVERT: B 252 ASP cc_start: 0.8429 (t0) cc_final: 0.8138 (t0) REVERT: E 42 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8303 (mmmm) REVERT: E 72 ASP cc_start: 0.8452 (t0) cc_final: 0.8066 (t0) REVERT: E 86 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8371 (ptp-170) REVERT: E 88 GLU cc_start: 0.9213 (pp20) cc_final: 0.8921 (pp20) REVERT: E 244 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8213 (tmmt) REVERT: G 12 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8197 (tmm-80) REVERT: G 13 LYS cc_start: 0.9401 (mmmm) cc_final: 0.8878 (mmmm) REVERT: G 17 GLN cc_start: 0.8205 (tp40) cc_final: 0.7682 (tp40) REVERT: G 21 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7255 (mt-10) REVERT: G 45 LYS cc_start: 0.9144 (mtmm) cc_final: 0.8890 (mppt) REVERT: R 32 ARG cc_start: 0.7657 (tpt170) cc_final: 0.7224 (tpt90) REVERT: R 68 TYR cc_start: 0.8841 (t80) cc_final: 0.7840 (t80) REVERT: R 185 GLN cc_start: 0.6671 (mp10) cc_final: 0.6433 (mp10) REVERT: R 187 GLU cc_start: 0.5747 (tm-30) cc_final: 0.4698 (tm-30) REVERT: R 198 HIS cc_start: 0.6631 (m170) cc_final: 0.6342 (m170) REVERT: R 200 CYS cc_start: 0.7399 (m) cc_final: 0.6392 (m) REVERT: R 204 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8167 (mm-30) REVERT: R 210 HIS cc_start: 0.8064 (m170) cc_final: 0.7843 (m170) REVERT: R 312 MET cc_start: 0.9239 (mtm) cc_final: 0.9031 (mtm) outliers start: 43 outliers final: 14 residues processed: 271 average time/residue: 0.5277 time to fit residues: 152.0858 Evaluate side-chains 223 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 264 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 80 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 186 GLN R 63 ASN R 156 GLN R 338 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065197 restraints weight = 21253.083| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.54 r_work: 0.2800 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9547 Z= 0.228 Angle : 0.662 10.191 12933 Z= 0.342 Chirality : 0.044 0.185 1471 Planarity : 0.005 0.062 1638 Dihedral : 4.201 20.512 1298 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.60 % Allowed : 19.28 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1181 helix: 1.72 (0.25), residues: 431 sheet: 0.12 (0.32), residues: 269 loop : -1.04 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.020 0.002 TYR E 190 PHE 0.019 0.002 PHE R 61 TRP 0.014 0.002 TRP B 174 HIS 0.008 0.002 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 9546) covalent geometry : angle 0.66218 (12931) SS BOND : bond 0.01597 ( 1) SS BOND : angle 1.70781 ( 2) hydrogen bonds : bond 0.03740 ( 465) hydrogen bonds : angle 4.68970 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.6999 (m-80) cc_final: 0.6679 (m-10) REVERT: A 247 ARG cc_start: 0.8623 (pmm-80) cc_final: 0.8295 (ppp80) REVERT: B 28 LYS cc_start: 0.8984 (tmmm) cc_final: 0.8754 (ttmm) REVERT: B 177 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 252 ASP cc_start: 0.8681 (t0) cc_final: 0.8354 (t0) REVERT: B 319 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8026 (ttm170) REVERT: E 42 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8256 (mmmm) REVERT: E 72 ASP cc_start: 0.8538 (t0) cc_final: 0.8309 (t0) REVERT: E 86 ARG cc_start: 0.8903 (mtt180) cc_final: 0.8622 (ptp-170) REVERT: E 234 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6967 (mt-10) REVERT: E 244 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8143 (tmmt) REVERT: G 20 MET cc_start: 0.9249 (ptp) cc_final: 0.8308 (ptm) REVERT: G 41 GLU cc_start: 0.8842 (pp20) cc_final: 0.8534 (pp20) REVERT: G 45 LYS cc_start: 0.9236 (mtmm) cc_final: 0.8993 (mppt) REVERT: R 32 ARG cc_start: 0.7534 (tpt170) cc_final: 0.7011 (tpt90) REVERT: R 50 LEU cc_start: 0.9407 (mt) cc_final: 0.9193 (pp) REVERT: R 68 TYR cc_start: 0.8859 (t80) cc_final: 0.8561 (t80) REVERT: R 72 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8016 (ppp80) REVERT: R 185 GLN cc_start: 0.6787 (mp10) cc_final: 0.6560 (mp10) REVERT: R 187 GLU cc_start: 0.5823 (tm-30) cc_final: 0.4834 (tm-30) REVERT: R 200 CYS cc_start: 0.7726 (m) cc_final: 0.6632 (m) REVERT: R 204 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8381 (mm-30) REVERT: R 210 HIS cc_start: 0.8220 (m170) cc_final: 0.7756 (m170) REVERT: R 295 MET cc_start: 0.8386 (ttt) cc_final: 0.8127 (ttm) REVERT: R 312 MET cc_start: 0.9266 (mtm) cc_final: 0.8992 (mtm) REVERT: R 337 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8332 (mp0) REVERT: R 341 LYS cc_start: 0.9317 (mmpt) cc_final: 0.8945 (mmtm) REVERT: R 342 ASN cc_start: 0.7558 (m110) cc_final: 0.7327 (t0) outliers start: 46 outliers final: 18 residues processed: 252 average time/residue: 0.5220 time to fit residues: 139.8417 Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 51 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: A 24 GLN A 52 GLN A 213 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 186 GLN E 194 ASN R 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068712 restraints weight = 21001.460| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.56 r_work: 0.2886 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9547 Z= 0.123 Angle : 0.602 8.312 12933 Z= 0.307 Chirality : 0.041 0.173 1471 Planarity : 0.004 0.036 1638 Dihedral : 3.940 18.109 1298 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.70 % Allowed : 21.78 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1181 helix: 1.97 (0.25), residues: 431 sheet: 0.29 (0.31), residues: 267 loop : -0.91 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.015 0.001 TYR R 157 PHE 0.017 0.001 PHE E 203 TRP 0.011 0.001 TRP R 170 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9546) covalent geometry : angle 0.60232 (12931) SS BOND : bond 0.00753 ( 1) SS BOND : angle 1.16592 ( 2) hydrogen bonds : bond 0.03215 ( 465) hydrogen bonds : angle 4.46272 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8529 (tp40) REVERT: A 185 PHE cc_start: 0.7092 (m-80) cc_final: 0.6774 (m-10) REVERT: A 247 ARG cc_start: 0.8600 (pmm-80) cc_final: 0.8349 (ppp80) REVERT: B 28 LYS cc_start: 0.8965 (tmmm) cc_final: 0.8730 (ttmm) REVERT: B 50 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8343 (mtp) REVERT: B 177 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8633 (mm-30) REVERT: B 239 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: B 252 ASP cc_start: 0.8594 (t0) cc_final: 0.8275 (t0) REVERT: B 319 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8111 (ttm170) REVERT: E 42 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8303 (mmmm) REVERT: E 72 ASP cc_start: 0.8536 (t0) cc_final: 0.8257 (t0) REVERT: E 234 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6909 (mt-10) REVERT: E 244 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8100 (tmmt) REVERT: G 12 ARG cc_start: 0.8993 (tmm-80) cc_final: 0.8782 (tmm-80) REVERT: G 13 LYS cc_start: 0.9432 (mmmm) cc_final: 0.8984 (mmmm) REVERT: G 19 LYS cc_start: 0.9525 (ttpp) cc_final: 0.9259 (tmmt) REVERT: G 41 GLU cc_start: 0.8836 (pp20) cc_final: 0.8495 (pp20) REVERT: G 45 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8975 (mppt) REVERT: G 57 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7425 (mp0) REVERT: R 32 ARG cc_start: 0.7577 (tpt170) cc_final: 0.6898 (tpt90) REVERT: R 76 MET cc_start: 0.8387 (mmt) cc_final: 0.8013 (mmt) REVERT: R 77 ARG cc_start: 0.8448 (mpt180) cc_final: 0.8167 (mpt180) REVERT: R 187 GLU cc_start: 0.5942 (tm-30) cc_final: 0.4990 (tm-30) REVERT: R 197 GLU cc_start: 0.7621 (tp30) cc_final: 0.7211 (tp30) REVERT: R 200 CYS cc_start: 0.7652 (m) cc_final: 0.6609 (m) REVERT: R 210 HIS cc_start: 0.8244 (m170) cc_final: 0.7736 (m170) REVERT: R 312 MET cc_start: 0.9267 (mtm) cc_final: 0.9013 (mtm) REVERT: R 341 LYS cc_start: 0.9319 (mmpt) cc_final: 0.9065 (mmpt) outliers start: 37 outliers final: 14 residues processed: 243 average time/residue: 0.5461 time to fit residues: 140.6520 Evaluate side-chains 212 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 194 ASN R 63 ASN R 81 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065006 restraints weight = 20956.991| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.54 r_work: 0.2877 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9547 Z= 0.218 Angle : 0.644 8.574 12933 Z= 0.331 Chirality : 0.043 0.177 1471 Planarity : 0.004 0.043 1638 Dihedral : 4.145 19.902 1298 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.90 % Allowed : 23.18 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1181 helix: 1.89 (0.25), residues: 431 sheet: 0.33 (0.31), residues: 272 loop : -0.85 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.020 0.002 TYR E 190 PHE 0.013 0.002 PHE R 61 TRP 0.012 0.002 TRP B 87 HIS 0.006 0.002 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9546) covalent geometry : angle 0.64391 (12931) SS BOND : bond 0.01189 ( 1) SS BOND : angle 1.40427 ( 2) hydrogen bonds : bond 0.03439 ( 465) hydrogen bonds : angle 4.47126 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8925 (m-30) cc_final: 0.8591 (m-30) REVERT: A 28 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8557 (tp-100) REVERT: A 185 PHE cc_start: 0.7205 (m-80) cc_final: 0.6899 (m-10) REVERT: B 28 LYS cc_start: 0.9063 (tmmm) cc_final: 0.8839 (ttmm) REVERT: B 177 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8618 (mm-30) REVERT: B 219 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8450 (mpp80) REVERT: B 252 ASP cc_start: 0.8677 (t0) cc_final: 0.8354 (t0) REVERT: B 319 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8144 (ttm170) REVERT: E 42 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8377 (mmmm) REVERT: E 72 ASP cc_start: 0.8581 (t0) cc_final: 0.8315 (t0) REVERT: E 234 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7130 (mt-10) REVERT: E 244 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8115 (tmmt) REVERT: G 16 GLU cc_start: 0.8882 (pp20) cc_final: 0.8512 (pp20) REVERT: G 19 LYS cc_start: 0.9564 (ttpp) cc_final: 0.9244 (tmmt) REVERT: G 41 GLU cc_start: 0.8909 (pp20) cc_final: 0.8701 (pp20) REVERT: G 57 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7415 (mp0) REVERT: R 32 ARG cc_start: 0.7656 (tpt170) cc_final: 0.6968 (tpt90) REVERT: R 68 TYR cc_start: 0.8894 (t80) cc_final: 0.8617 (t80) REVERT: R 76 MET cc_start: 0.8499 (mmt) cc_final: 0.8095 (mmt) REVERT: R 160 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7624 (tpm170) REVERT: R 187 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5228 (tm-30) REVERT: R 210 HIS cc_start: 0.8333 (m170) cc_final: 0.7779 (m170) REVERT: R 225 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8508 (tt) REVERT: R 240 GLU cc_start: 0.8743 (tp30) cc_final: 0.8355 (tm-30) REVERT: R 312 MET cc_start: 0.9317 (mtm) cc_final: 0.9014 (mtm) outliers start: 39 outliers final: 24 residues processed: 233 average time/residue: 0.5641 time to fit residues: 139.5564 Evaluate side-chains 218 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 132 GLU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 294 MET Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN R 63 ASN R 211 GLN ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.090057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062925 restraints weight = 21122.439| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.52 r_work: 0.2822 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9547 Z= 0.260 Angle : 0.684 9.124 12933 Z= 0.353 Chirality : 0.045 0.185 1471 Planarity : 0.004 0.041 1638 Dihedral : 4.379 21.809 1298 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.80 % Allowed : 23.18 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.24), residues: 1181 helix: 1.74 (0.25), residues: 433 sheet: 0.42 (0.32), residues: 261 loop : -0.83 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 12 TYR 0.023 0.002 TYR E 190 PHE 0.015 0.002 PHE B 340 TRP 0.014 0.002 TRP B 87 HIS 0.006 0.002 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9546) covalent geometry : angle 0.68347 (12931) SS BOND : bond 0.01374 ( 1) SS BOND : angle 1.68303 ( 2) hydrogen bonds : bond 0.03650 ( 465) hydrogen bonds : angle 4.55723 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8633 (mt-10) REVERT: A 22 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8890 (tp-100) REVERT: A 28 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8585 (tp-100) REVERT: A 53 MET cc_start: 0.8592 (mtp) cc_final: 0.8358 (ttp) REVERT: A 185 PHE cc_start: 0.7186 (m-80) cc_final: 0.6905 (m-10) REVERT: B 177 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 252 ASP cc_start: 0.8778 (t0) cc_final: 0.8482 (t0) REVERT: B 319 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8186 (ttm170) REVERT: E 42 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8467 (mmmm) REVERT: E 72 ASP cc_start: 0.8526 (t0) cc_final: 0.7975 (t0) REVERT: E 234 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7305 (mt-10) REVERT: E 244 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8091 (tmmt) REVERT: G 16 GLU cc_start: 0.8832 (pp20) cc_final: 0.8587 (pp20) REVERT: G 19 LYS cc_start: 0.9550 (ttpp) cc_final: 0.9245 (tmmt) REVERT: G 57 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7441 (mp0) REVERT: R 32 ARG cc_start: 0.7601 (tpt170) cc_final: 0.7099 (tpt90) REVERT: R 72 ARG cc_start: 0.8511 (ptm160) cc_final: 0.7865 (ppp80) REVERT: R 76 MET cc_start: 0.8559 (mmt) cc_final: 0.8159 (mmt) REVERT: R 91 ASP cc_start: 0.8829 (t70) cc_final: 0.8399 (t70) REVERT: R 160 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7656 (tpm170) REVERT: R 210 HIS cc_start: 0.8402 (m170) cc_final: 0.7808 (m170) REVERT: R 312 MET cc_start: 0.9346 (mtm) cc_final: 0.9058 (mtm) outliers start: 48 outliers final: 21 residues processed: 229 average time/residue: 0.5171 time to fit residues: 126.1957 Evaluate side-chains 209 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.065224 restraints weight = 21206.501| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.54 r_work: 0.2862 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9547 Z= 0.130 Angle : 0.640 10.390 12933 Z= 0.326 Chirality : 0.042 0.165 1471 Planarity : 0.003 0.041 1638 Dihedral : 4.163 18.765 1298 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.20 % Allowed : 25.07 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.25), residues: 1181 helix: 1.81 (0.25), residues: 433 sheet: 0.57 (0.33), residues: 258 loop : -0.73 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.020 0.001 TYR R 68 PHE 0.013 0.001 PHE R 61 TRP 0.013 0.001 TRP R 205 HIS 0.007 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9546) covalent geometry : angle 0.64023 (12931) SS BOND : bond 0.00663 ( 1) SS BOND : angle 1.00854 ( 2) hydrogen bonds : bond 0.03348 ( 465) hydrogen bonds : angle 4.41305 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8970 (m-30) cc_final: 0.8648 (m-30) REVERT: A 22 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8914 (tp-100) REVERT: A 28 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8496 (tp-100) REVERT: A 185 PHE cc_start: 0.7165 (m-80) cc_final: 0.6876 (m-10) REVERT: A 247 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7760 (ppp80) REVERT: B 15 GLU cc_start: 0.9322 (tp30) cc_final: 0.9108 (tp30) REVERT: B 50 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8461 (mtp) REVERT: B 177 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8615 (mm-30) REVERT: B 239 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: B 252 ASP cc_start: 0.8656 (t0) cc_final: 0.8413 (t0) REVERT: B 319 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8198 (ttm170) REVERT: E 42 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8425 (mmmm) REVERT: E 64 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8539 (ttmm) REVERT: E 72 ASP cc_start: 0.8497 (t0) cc_final: 0.7956 (t0) REVERT: E 92 MET cc_start: 0.8241 (ttm) cc_final: 0.7915 (tpp) REVERT: E 223 ASP cc_start: 0.8351 (m-30) cc_final: 0.7907 (m-30) REVERT: E 234 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7051 (mt-10) REVERT: E 244 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8050 (tmmt) REVERT: G 16 GLU cc_start: 0.9016 (pp20) cc_final: 0.8508 (pp20) REVERT: G 19 LYS cc_start: 0.9530 (ttpp) cc_final: 0.9264 (tmmt) REVERT: G 20 MET cc_start: 0.9008 (ptp) cc_final: 0.8722 (pmm) REVERT: G 28 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8344 (mmpt) REVERT: G 57 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7311 (mp0) REVERT: R 32 ARG cc_start: 0.7544 (tpt170) cc_final: 0.7040 (tpt90) REVERT: R 68 TYR cc_start: 0.9047 (t80) cc_final: 0.8834 (t80) REVERT: R 72 ARG cc_start: 0.8395 (ptm160) cc_final: 0.7787 (ppp80) REVERT: R 76 MET cc_start: 0.8522 (mmt) cc_final: 0.8159 (mmt) REVERT: R 91 ASP cc_start: 0.8824 (t70) cc_final: 0.8375 (t70) REVERT: R 155 TRP cc_start: 0.8961 (p-90) cc_final: 0.8581 (p-90) REVERT: R 160 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7603 (tpm170) REVERT: R 210 HIS cc_start: 0.8472 (m170) cc_final: 0.7914 (m170) REVERT: R 225 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8444 (tt) REVERT: R 312 MET cc_start: 0.9300 (mtm) cc_final: 0.8956 (mtm) outliers start: 32 outliers final: 17 residues processed: 230 average time/residue: 0.4872 time to fit residues: 119.6159 Evaluate side-chains 216 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.062690 restraints weight = 21339.084| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.53 r_work: 0.2800 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9547 Z= 0.233 Angle : 0.700 10.512 12933 Z= 0.360 Chirality : 0.044 0.170 1471 Planarity : 0.004 0.044 1638 Dihedral : 4.272 20.350 1296 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.80 % Allowed : 25.97 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1181 helix: 1.74 (0.25), residues: 432 sheet: 0.49 (0.33), residues: 260 loop : -0.71 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 356 TYR 0.020 0.002 TYR E 190 PHE 0.014 0.002 PHE B 340 TRP 0.013 0.001 TRP R 170 HIS 0.007 0.002 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9546) covalent geometry : angle 0.69944 (12931) SS BOND : bond 0.01272 ( 1) SS BOND : angle 1.49825 ( 2) hydrogen bonds : bond 0.03540 ( 465) hydrogen bonds : angle 4.46777 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8932 (m-30) cc_final: 0.8599 (m-30) REVERT: A 20 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8618 (mt-10) REVERT: A 22 GLN cc_start: 0.9140 (tp-100) cc_final: 0.8922 (tp-100) REVERT: A 28 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8590 (tp-100) REVERT: A 185 PHE cc_start: 0.7157 (m-80) cc_final: 0.6874 (m-10) REVERT: A 247 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7894 (ppp80) REVERT: B 15 GLU cc_start: 0.9373 (tp30) cc_final: 0.9156 (tp30) REVERT: B 177 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8596 (mm-30) REVERT: B 252 ASP cc_start: 0.8754 (t0) cc_final: 0.8482 (t0) REVERT: B 319 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8140 (ttm170) REVERT: E 42 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8373 (mmmm) REVERT: E 64 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8535 (ttmm) REVERT: E 72 ASP cc_start: 0.8500 (t0) cc_final: 0.7947 (t0) REVERT: E 92 MET cc_start: 0.8218 (ttm) cc_final: 0.7876 (tpp) REVERT: E 201 ASP cc_start: 0.8904 (p0) cc_final: 0.8578 (t70) REVERT: E 223 ASP cc_start: 0.8400 (m-30) cc_final: 0.7356 (m-30) REVERT: E 234 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7227 (mt-10) REVERT: E 244 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8089 (tmmt) REVERT: G 13 LYS cc_start: 0.9463 (mmmm) cc_final: 0.9190 (mmmm) REVERT: G 16 GLU cc_start: 0.8991 (pp20) cc_final: 0.8380 (pp20) REVERT: G 19 LYS cc_start: 0.9507 (ttpp) cc_final: 0.9264 (tmmt) REVERT: G 20 MET cc_start: 0.8952 (ptp) cc_final: 0.8703 (pmm) REVERT: G 28 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8397 (mmpt) REVERT: G 57 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7446 (mp0) REVERT: R 32 ARG cc_start: 0.7504 (tpt170) cc_final: 0.6998 (tpt90) REVERT: R 68 TYR cc_start: 0.9062 (t80) cc_final: 0.8848 (t80) REVERT: R 72 ARG cc_start: 0.8477 (ptm160) cc_final: 0.7788 (ppp80) REVERT: R 76 MET cc_start: 0.8552 (mmt) cc_final: 0.8255 (mmt) REVERT: R 91 ASP cc_start: 0.8861 (t70) cc_final: 0.8460 (t70) REVERT: R 160 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7643 (tpm170) REVERT: R 210 HIS cc_start: 0.8498 (m170) cc_final: 0.7958 (m170) REVERT: R 225 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8441 (tt) REVERT: R 312 MET cc_start: 0.9329 (mtm) cc_final: 0.9020 (mtm) outliers start: 38 outliers final: 24 residues processed: 225 average time/residue: 0.5416 time to fit residues: 129.4376 Evaluate side-chains 218 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 306 ASP Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.091634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065079 restraints weight = 21151.048| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.54 r_work: 0.2856 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9547 Z= 0.137 Angle : 0.691 11.388 12933 Z= 0.352 Chirality : 0.043 0.197 1471 Planarity : 0.004 0.054 1638 Dihedral : 4.147 19.630 1296 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.80 % Allowed : 27.27 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.25), residues: 1181 helix: 1.72 (0.25), residues: 434 sheet: 0.68 (0.33), residues: 250 loop : -0.68 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.018 0.001 TYR R 68 PHE 0.014 0.001 PHE R 61 TRP 0.013 0.001 TRP R 170 HIS 0.007 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9546) covalent geometry : angle 0.69042 (12931) SS BOND : bond 0.00821 ( 1) SS BOND : angle 1.13105 ( 2) hydrogen bonds : bond 0.03407 ( 465) hydrogen bonds : angle 4.39797 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8947 (m-30) cc_final: 0.8588 (m-30) REVERT: A 20 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8587 (mt-10) REVERT: A 22 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8913 (tp-100) REVERT: A 28 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8509 (tp-100) REVERT: A 185 PHE cc_start: 0.7170 (m-80) cc_final: 0.6884 (m-10) REVERT: A 247 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7860 (ppp80) REVERT: B 15 GLU cc_start: 0.9367 (tp30) cc_final: 0.9108 (tp30) REVERT: B 177 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8641 (mm-30) REVERT: B 252 ASP cc_start: 0.8647 (t0) cc_final: 0.8422 (t0) REVERT: B 319 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8221 (ttm170) REVERT: B 330 MET cc_start: 0.9005 (tpp) cc_final: 0.8607 (mmm) REVERT: E 42 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8375 (mmmm) REVERT: E 72 ASP cc_start: 0.8493 (t0) cc_final: 0.7939 (t0) REVERT: E 92 MET cc_start: 0.8226 (ttm) cc_final: 0.7856 (tpp) REVERT: E 201 ASP cc_start: 0.8927 (p0) cc_final: 0.8607 (t70) REVERT: E 234 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7074 (mt-10) REVERT: E 244 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8040 (tmmt) REVERT: G 13 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9186 (mmmm) REVERT: G 16 GLU cc_start: 0.9014 (pp20) cc_final: 0.8612 (pp20) REVERT: G 19 LYS cc_start: 0.9495 (ttpp) cc_final: 0.9244 (tmmt) REVERT: G 28 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8399 (mmpt) REVERT: G 57 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7410 (mp0) REVERT: R 32 ARG cc_start: 0.7479 (tpt170) cc_final: 0.6898 (tpt90) REVERT: R 68 TYR cc_start: 0.9066 (t80) cc_final: 0.8827 (t80) REVERT: R 72 ARG cc_start: 0.8468 (ptm160) cc_final: 0.7719 (ptm-80) REVERT: R 76 MET cc_start: 0.8573 (mmt) cc_final: 0.8188 (mmt) REVERT: R 77 ARG cc_start: 0.8360 (mpt180) cc_final: 0.8119 (mtt90) REVERT: R 91 ASP cc_start: 0.8811 (t70) cc_final: 0.8495 (t70) REVERT: R 103 MET cc_start: 0.9172 (mmm) cc_final: 0.8915 (mtm) REVERT: R 155 TRP cc_start: 0.8966 (p-90) cc_final: 0.8595 (p-90) REVERT: R 160 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7568 (tpm170) REVERT: R 225 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8458 (tt) REVERT: R 312 MET cc_start: 0.9313 (mtm) cc_final: 0.8996 (mtm) outliers start: 28 outliers final: 15 residues processed: 220 average time/residue: 0.5252 time to fit residues: 122.9259 Evaluate side-chains 208 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 0.0070 chunk 20 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.065705 restraints weight = 21144.169| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.54 r_work: 0.2874 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9547 Z= 0.140 Angle : 0.694 9.677 12933 Z= 0.359 Chirality : 0.043 0.188 1471 Planarity : 0.004 0.097 1638 Dihedral : 4.089 17.986 1296 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 28.27 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1181 helix: 1.71 (0.25), residues: 435 sheet: 0.64 (0.32), residues: 258 loop : -0.72 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 12 TYR 0.017 0.001 TYR R 68 PHE 0.015 0.001 PHE R 61 TRP 0.014 0.001 TRP R 205 HIS 0.009 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9546) covalent geometry : angle 0.69373 (12931) SS BOND : bond 0.00658 ( 1) SS BOND : angle 0.84320 ( 2) hydrogen bonds : bond 0.03361 ( 465) hydrogen bonds : angle 4.39341 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8938 (m-30) cc_final: 0.8604 (m-30) REVERT: A 20 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 22 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8933 (tp-100) REVERT: A 28 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8520 (tp-100) REVERT: A 185 PHE cc_start: 0.7211 (m-80) cc_final: 0.6927 (m-10) REVERT: A 247 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7845 (ppp80) REVERT: B 15 GLU cc_start: 0.9370 (tp30) cc_final: 0.9137 (tp30) REVERT: B 64 TYR cc_start: 0.8929 (m-80) cc_final: 0.8641 (m-80) REVERT: B 177 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 319 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8208 (ttm170) REVERT: B 330 MET cc_start: 0.8994 (tpp) cc_final: 0.8596 (mmm) REVERT: E 42 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8381 (mmmm) REVERT: E 72 ASP cc_start: 0.8517 (t0) cc_final: 0.7977 (t0) REVERT: E 92 MET cc_start: 0.8213 (ttm) cc_final: 0.7881 (tpp) REVERT: E 201 ASP cc_start: 0.8926 (p0) cc_final: 0.8622 (t0) REVERT: E 234 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7046 (mt-10) REVERT: E 244 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8572 (ttpp) REVERT: G 13 LYS cc_start: 0.9500 (mmmm) cc_final: 0.9208 (mmmm) REVERT: G 16 GLU cc_start: 0.9104 (pp20) cc_final: 0.8552 (pp20) REVERT: G 19 LYS cc_start: 0.9494 (ttpp) cc_final: 0.9269 (tmmt) REVERT: G 20 MET cc_start: 0.9003 (ptp) cc_final: 0.8680 (pmm) REVERT: G 28 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8596 (mmmm) REVERT: G 57 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7454 (mp0) REVERT: R 68 TYR cc_start: 0.9061 (t80) cc_final: 0.8780 (t80) REVERT: R 72 ARG cc_start: 0.8511 (ptm160) cc_final: 0.7770 (ptm-80) REVERT: R 76 MET cc_start: 0.8531 (mmt) cc_final: 0.8261 (mmt) REVERT: R 77 ARG cc_start: 0.8390 (mpt180) cc_final: 0.8087 (mtt90) REVERT: R 91 ASP cc_start: 0.8785 (t70) cc_final: 0.8340 (t70) REVERT: R 120 MET cc_start: 0.8740 (tmm) cc_final: 0.8221 (tmm) REVERT: R 155 TRP cc_start: 0.8947 (p-90) cc_final: 0.8576 (p-90) REVERT: R 160 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7549 (tpm170) REVERT: R 225 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8448 (tt) REVERT: R 312 MET cc_start: 0.9325 (mtm) cc_final: 0.8984 (mtm) outliers start: 20 outliers final: 16 residues processed: 214 average time/residue: 0.5243 time to fit residues: 119.1537 Evaluate side-chains 209 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066940 restraints weight = 21290.857| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.51 r_work: 0.2888 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9547 Z= 0.140 Angle : 0.696 10.240 12933 Z= 0.356 Chirality : 0.043 0.191 1471 Planarity : 0.004 0.056 1638 Dihedral : 4.044 18.212 1296 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.40 % Allowed : 28.27 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1181 helix: 1.74 (0.25), residues: 435 sheet: 0.56 (0.32), residues: 265 loop : -0.62 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.018 0.001 TYR R 36 PHE 0.015 0.001 PHE R 61 TRP 0.018 0.001 TRP R 205 HIS 0.008 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9546) covalent geometry : angle 0.69576 (12931) SS BOND : bond 0.00725 ( 1) SS BOND : angle 1.00026 ( 2) hydrogen bonds : bond 0.03274 ( 465) hydrogen bonds : angle 4.37604 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.82 seconds wall clock time: 67 minutes 26.34 seconds (4046.34 seconds total)