Starting phenix.real_space_refine on Wed Mar 12 12:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcp_29940/03_2025/8gcp_29940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcp_29940/03_2025/8gcp_29940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gcp_29940/03_2025/8gcp_29940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcp_29940/03_2025/8gcp_29940.map" model { file = "/net/cci-nas-00/data/ceres_data/8gcp_29940/03_2025/8gcp_29940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcp_29940/03_2025/8gcp_29940.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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 57 5.16 5 C 5047 2.51 5 N 1340 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7921 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1548 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'PHE%COO:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2476 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 362 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1614 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Chain: "R" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1896 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.65 Number of scatterers: 7921 At special positions: 0 Unit cell: (90.95, 119.85, 124.95, 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 57 16.00 O 1477 8.00 N 1340 7.00 C 5047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 934.5 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 33.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.527A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.541A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.716A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.604A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.143A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.787A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.980A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.587A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.157A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.831A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.521A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 45 removed outlier: 3.975A pdb=" N GLY R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 82 removed outlier: 4.375A pdb=" N THR R 56 " --> pdb=" O THR R 52 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 91 through 113 removed outlier: 3.983A pdb=" N PHE R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 123 removed outlier: 3.596A pdb=" N ILE R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 131 removed outlier: 3.655A pdb=" N VAL R 131 " --> pdb=" O TYR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 152 Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.645A pdb=" N MET R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 218 removed outlier: 4.336A pdb=" N SER R 185 " --> pdb=" O HIS R 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU R 211 " --> pdb=" O CYS R 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG R 212 " --> pdb=" O GLY R 208 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.834A pdb=" N LEU R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU R 279 " --> pdb=" O ILE R 275 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 311 through 318 Processing helix chain 'R' and resid 319 through 324 removed outlier: 3.509A pdb=" N ILE R 323 " --> pdb=" O SER R 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.536A pdb=" N VAL A 34 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.831A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.907A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.049A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.765A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 6.411A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.776A pdb=" N VAL E 12 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.722A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.729A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 162 through 163 removed outlier: 3.539A pdb=" N ARG R 162 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE R 171 " --> pdb=" O ARG R 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 365 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.44: 2213 1.44 - 1.57: 4472 1.57 - 1.70: 2 1.70 - 1.82: 79 Bond restraints: 8076 Sorted by residual: bond pdb=" C13 P2E R 501 " pdb=" C14 P2E R 501 " ideal model delta sigma weight residual 1.329 1.530 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 P2E R 501 " pdb=" C6 P2E R 501 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C CYS R 59 " pdb=" N GLY R 60 " ideal model delta sigma weight residual 1.334 1.228 0.106 1.32e-02 5.74e+03 6.41e+01 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.453 1.519 -0.066 1.31e-02 5.83e+03 2.57e+01 bond pdb=" CA VAL B 307 " pdb=" C VAL B 307 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.27e-02 6.20e+03 2.33e+01 ... (remaining 8071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 10633 2.90 - 5.81: 313 5.81 - 8.71: 61 8.71 - 11.61: 16 11.61 - 14.52: 5 Bond angle restraints: 11028 Sorted by residual: angle pdb=" C GLN R 299 " pdb=" N PRO R 300 " pdb=" CA PRO R 300 " ideal model delta sigma weight residual 120.51 130.47 -9.96 1.26e+00 6.30e-01 6.25e+01 angle pdb=" N PHE R 217 " pdb=" CA PHE R 217 " pdb=" C PHE R 217 " ideal model delta sigma weight residual 112.90 123.12 -10.22 1.31e+00 5.83e-01 6.09e+01 angle pdb=" N SER R 307 " pdb=" CA SER R 307 " pdb=" C SER R 307 " ideal model delta sigma weight residual 112.92 122.34 -9.42 1.23e+00 6.61e-01 5.87e+01 angle pdb=" N LEU R 302 " pdb=" CA LEU R 302 " pdb=" C LEU R 302 " ideal model delta sigma weight residual 108.56 121.01 -12.45 1.74e+00 3.30e-01 5.12e+01 angle pdb=" N ALA C 56 " pdb=" CA ALA C 56 " pdb=" C ALA C 56 " ideal model delta sigma weight residual 112.38 121.07 -8.69 1.22e+00 6.72e-01 5.07e+01 ... (remaining 11023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4270 17.73 - 35.45: 370 35.45 - 53.18: 61 53.18 - 70.91: 5 70.91 - 88.63: 4 Dihedral angle restraints: 4710 sinusoidal: 1503 harmonic: 3207 Sorted by residual: dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C ALA C 56 " pdb=" N ALA C 56 " pdb=" CA ALA C 56 " pdb=" CB ALA C 56 " ideal model delta harmonic sigma weight residual -122.60 -133.80 11.20 0 2.50e+00 1.60e-01 2.01e+01 dihedral pdb=" CA CYS A 286 " pdb=" C CYS A 286 " pdb=" N TYR A 287 " pdb=" CA TYR A 287 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1225 0.120 - 0.240: 78 0.240 - 0.360: 13 0.360 - 0.480: 7 0.480 - 0.600: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA ALA C 56 " pdb=" N ALA C 56 " pdb=" C ALA C 56 " pdb=" CB ALA C 56 " both_signs ideal model delta sigma weight residual False 2.48 1.88 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CA PHE R 217 " pdb=" N PHE R 217 " pdb=" C PHE R 217 " pdb=" CB PHE R 217 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA MET E 192 " pdb=" N MET E 192 " pdb=" C MET E 192 " pdb=" CB MET E 192 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1321 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 501 " 0.153 2.00e-02 2.50e+03 3.20e-01 1.02e+03 pdb=" C5 P2E R 501 " -0.424 2.00e-02 2.50e+03 pdb=" C6 P2E R 501 " 0.427 2.00e-02 2.50e+03 pdb=" C7 P2E R 501 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 174 " -0.031 2.00e-02 2.50e+03 2.69e-02 1.80e+01 pdb=" CG TRP R 174 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP R 174 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP R 174 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 174 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 174 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 174 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 236 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.052 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1723 2.77 - 3.31: 6848 3.31 - 3.84: 12533 3.84 - 4.37: 14162 4.37 - 4.90: 25231 Nonbonded interactions: 60497 Sorted by model distance: nonbonded pdb=" OG1 THR R 64 " pdb=" OH TYR R 144 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.268 3.040 nonbonded pdb=" O THR E 243 " pdb=" CG2 THR E 243 " model vdw 2.294 3.460 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.303 3.040 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.312 3.040 ... (remaining 60492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.011 0.201 8076 Z= 0.713 Angle : 1.264 14.515 11028 Z= 0.724 Chirality : 0.077 0.600 1324 Planarity : 0.012 0.320 1403 Dihedral : 13.822 88.634 2632 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.67 % Allowed : 2.02 % Favored : 97.31 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.24), residues: 1086 helix: -1.49 (0.25), residues: 355 sheet: -0.16 (0.34), residues: 244 loop : -2.40 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP R 174 HIS 0.017 0.003 HIS B 311 PHE 0.029 0.003 PHE A 196 TYR 0.027 0.003 TYR B 105 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.771 Fit side-chains REVERT: A 270 LYS cc_start: 0.7003 (pttm) cc_final: 0.6784 (pttm) REVERT: B 209 LYS cc_start: 0.8645 (mttm) cc_final: 0.7098 (mtmt) REVERT: B 228 ASP cc_start: 0.7436 (p0) cc_final: 0.7222 (p0) REVERT: E 83 MET cc_start: 0.6809 (mtm) cc_final: 0.6396 (mtm) REVERT: E 243 THR cc_start: 0.8296 (t) cc_final: 0.8002 (m) outliers start: 5 outliers final: 1 residues processed: 144 average time/residue: 0.2070 time to fit residues: 40.2953 Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 331 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.169447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135278 restraints weight = 11024.915| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.18 r_work: 0.3408 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8076 Z= 0.199 Angle : 0.609 12.145 11028 Z= 0.317 Chirality : 0.042 0.170 1324 Planarity : 0.004 0.056 1403 Dihedral : 6.581 83.950 1202 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 9.83 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1086 helix: 0.40 (0.28), residues: 348 sheet: -0.31 (0.34), residues: 249 loop : -2.13 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 174 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.002 PHE A 336 TYR 0.013 0.001 TYR R 144 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.939 Fit side-chains REVERT: A 38 LEU cc_start: 0.8780 (tp) cc_final: 0.8520 (tt) REVERT: B 52 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7995 (mtt-85) REVERT: B 124 TYR cc_start: 0.8620 (m-80) cc_final: 0.8162 (m-80) REVERT: B 129 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7332 (mmm-85) REVERT: B 209 LYS cc_start: 0.8743 (mttm) cc_final: 0.7229 (mtmt) REVERT: B 228 ASP cc_start: 0.8034 (p0) cc_final: 0.7828 (p0) outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 0.2633 time to fit residues: 54.0542 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.168674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134646 restraints weight = 11182.637| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.25 r_work: 0.3386 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8076 Z= 0.225 Angle : 0.589 10.013 11028 Z= 0.305 Chirality : 0.042 0.147 1324 Planarity : 0.004 0.048 1403 Dihedral : 6.193 82.291 1202 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.48 % Allowed : 15.61 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.26), residues: 1086 helix: 1.03 (0.30), residues: 349 sheet: -0.09 (0.34), residues: 242 loop : -2.06 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 174 HIS 0.006 0.001 HIS E 35 PHE 0.019 0.002 PHE E 29 TYR 0.015 0.001 TYR B 105 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.918 Fit side-chains REVERT: A 38 LEU cc_start: 0.8767 (tp) cc_final: 0.8497 (tt) REVERT: B 52 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7991 (mtt-85) REVERT: B 129 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7246 (mmm-85) REVERT: B 209 LYS cc_start: 0.8752 (mttm) cc_final: 0.7256 (mtmt) REVERT: B 228 ASP cc_start: 0.8024 (p0) cc_final: 0.7811 (p0) REVERT: B 268 ASN cc_start: 0.7540 (m110) cc_final: 0.7250 (m-40) outliers start: 11 outliers final: 7 residues processed: 149 average time/residue: 0.2023 time to fit residues: 40.6538 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain R residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 0.0020 chunk 78 optimal weight: 0.0030 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139197 restraints weight = 11055.082| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.24 r_work: 0.3444 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8076 Z= 0.126 Angle : 0.502 8.287 11028 Z= 0.260 Chirality : 0.040 0.132 1324 Planarity : 0.003 0.047 1403 Dihedral : 5.657 80.385 1202 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.21 % Allowed : 17.36 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1086 helix: 1.37 (0.30), residues: 354 sheet: 0.24 (0.34), residues: 241 loop : -1.92 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE E 29 TYR 0.007 0.001 TYR E 102 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.788 Fit side-chains REVERT: A 38 LEU cc_start: 0.8795 (tp) cc_final: 0.8445 (tt) REVERT: A 197 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7790 (ptpt) REVERT: B 127 LYS cc_start: 0.8470 (mttt) cc_final: 0.8158 (mttp) REVERT: B 134 ARG cc_start: 0.8150 (ptt-90) cc_final: 0.7933 (ptt-90) REVERT: B 209 LYS cc_start: 0.8604 (mttm) cc_final: 0.7217 (mtmt) REVERT: B 268 ASN cc_start: 0.7549 (m110) cc_final: 0.7254 (m-40) REVERT: E 83 MET cc_start: 0.6927 (mtm) cc_final: 0.6423 (mtm) REVERT: R 27 MET cc_start: 0.4927 (mtt) cc_final: 0.4720 (mtt) outliers start: 9 outliers final: 4 residues processed: 143 average time/residue: 0.2228 time to fit residues: 41.7951 Evaluate side-chains 137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain R residue 110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134290 restraints weight = 10998.588| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.14 r_work: 0.3406 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8076 Z= 0.198 Angle : 0.546 7.726 11028 Z= 0.282 Chirality : 0.042 0.147 1324 Planarity : 0.003 0.040 1403 Dihedral : 5.683 83.820 1202 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 17.77 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1086 helix: 1.55 (0.30), residues: 355 sheet: 0.21 (0.34), residues: 249 loop : -1.84 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.004 0.001 HIS E 167 PHE 0.019 0.002 PHE E 29 TYR 0.011 0.001 TYR B 105 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.837 Fit side-chains REVERT: A 38 LEU cc_start: 0.8790 (tp) cc_final: 0.8523 (tt) REVERT: A 197 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7836 (ptpt) REVERT: A 225 VAL cc_start: 0.7922 (t) cc_final: 0.7718 (t) REVERT: A 270 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6844 (pttm) REVERT: B 50 THR cc_start: 0.8338 (m) cc_final: 0.8068 (m) REVERT: B 209 LYS cc_start: 0.8706 (mttm) cc_final: 0.7208 (mtmt) REVERT: B 268 ASN cc_start: 0.7598 (m110) cc_final: 0.7300 (m-40) REVERT: E 83 MET cc_start: 0.6995 (mtm) cc_final: 0.6450 (mtm) REVERT: R 27 MET cc_start: 0.4900 (mtt) cc_final: 0.4696 (mtt) REVERT: R 140 LEU cc_start: 0.4389 (mp) cc_final: 0.4106 (mt) outliers start: 21 outliers final: 10 residues processed: 144 average time/residue: 0.2204 time to fit residues: 42.2016 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 218 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 24 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136543 restraints weight = 10914.701| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.93 r_work: 0.3443 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8076 Z= 0.167 Angle : 0.519 6.852 11028 Z= 0.269 Chirality : 0.042 0.235 1324 Planarity : 0.003 0.039 1403 Dihedral : 5.496 87.446 1200 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 18.98 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 1086 helix: 1.65 (0.30), residues: 361 sheet: 0.28 (0.34), residues: 248 loop : -1.74 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.020 0.001 PHE E 29 TYR 0.008 0.001 TYR E 173 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.749 Fit side-chains REVERT: A 197 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7873 (ptpt) REVERT: A 225 VAL cc_start: 0.7931 (t) cc_final: 0.7712 (t) REVERT: A 270 LYS cc_start: 0.6964 (pttm) cc_final: 0.6757 (pttm) REVERT: B 50 THR cc_start: 0.8250 (m) cc_final: 0.8020 (m) REVERT: B 209 LYS cc_start: 0.8679 (mttm) cc_final: 0.7330 (mtmt) REVERT: B 268 ASN cc_start: 0.7532 (m110) cc_final: 0.7238 (m-40) REVERT: E 83 MET cc_start: 0.6967 (mtm) cc_final: 0.6466 (mtm) outliers start: 13 outliers final: 8 residues processed: 138 average time/residue: 0.2271 time to fit residues: 40.9227 Evaluate side-chains 136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 chunk 26 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136982 restraints weight = 11009.581| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.10 r_work: 0.3459 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8076 Z= 0.136 Angle : 0.500 7.965 11028 Z= 0.260 Chirality : 0.041 0.218 1324 Planarity : 0.003 0.037 1403 Dihedral : 5.238 88.338 1200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.75 % Allowed : 19.65 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 1086 helix: 1.85 (0.30), residues: 356 sheet: 0.31 (0.34), residues: 250 loop : -1.66 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE E 29 TYR 0.010 0.001 TYR E 173 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.779 Fit side-chains REVERT: A 197 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7768 (ptpt) REVERT: A 225 VAL cc_start: 0.7899 (t) cc_final: 0.7666 (t) REVERT: A 270 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6679 (pttm) REVERT: B 50 THR cc_start: 0.8232 (m) cc_final: 0.8031 (m) REVERT: B 209 LYS cc_start: 0.8636 (mttm) cc_final: 0.7259 (mtmt) REVERT: B 268 ASN cc_start: 0.7548 (m110) cc_final: 0.7247 (m-40) REVERT: B 280 LYS cc_start: 0.8519 (tttp) cc_final: 0.8092 (mtpt) REVERT: E 83 MET cc_start: 0.6936 (mtm) cc_final: 0.6464 (mtm) REVERT: R 140 LEU cc_start: 0.4509 (mp) cc_final: 0.3960 (mp) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 0.2141 time to fit residues: 40.1341 Evaluate side-chains 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138850 restraints weight = 10956.405| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.00 r_work: 0.3458 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8076 Z= 0.153 Angle : 0.508 7.806 11028 Z= 0.264 Chirality : 0.041 0.215 1324 Planarity : 0.003 0.037 1403 Dihedral : 5.110 84.413 1200 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.42 % Allowed : 20.19 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 1086 helix: 2.00 (0.30), residues: 354 sheet: 0.34 (0.34), residues: 252 loop : -1.65 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE E 29 TYR 0.009 0.001 TYR R 94 ARG 0.005 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.787 Fit side-chains REVERT: A 197 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7787 (ptpt) REVERT: A 225 VAL cc_start: 0.7946 (t) cc_final: 0.7711 (t) REVERT: A 270 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6718 (pttm) REVERT: B 209 LYS cc_start: 0.8675 (mttm) cc_final: 0.7290 (mtmt) REVERT: B 268 ASN cc_start: 0.7566 (m110) cc_final: 0.7247 (m-40) REVERT: E 83 MET cc_start: 0.6980 (mtm) cc_final: 0.6495 (mtm) REVERT: R 126 PHE cc_start: 0.6957 (t80) cc_final: 0.6715 (t80) REVERT: R 140 LEU cc_start: 0.4517 (mp) cc_final: 0.3937 (mp) outliers start: 18 outliers final: 13 residues processed: 146 average time/residue: 0.2121 time to fit residues: 41.0740 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.0000 chunk 71 optimal weight: 0.0060 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.173756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139885 restraints weight = 11001.008| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.00 r_work: 0.3479 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8076 Z= 0.115 Angle : 0.484 7.665 11028 Z= 0.250 Chirality : 0.041 0.199 1324 Planarity : 0.003 0.037 1403 Dihedral : 4.861 80.603 1200 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.88 % Allowed : 21.00 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1086 helix: 2.16 (0.30), residues: 350 sheet: 0.43 (0.34), residues: 253 loop : -1.57 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.000 HIS E 35 PHE 0.016 0.001 PHE E 29 TYR 0.012 0.001 TYR E 173 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.769 Fit side-chains REVERT: A 197 LYS cc_start: 0.8046 (ptpt) cc_final: 0.7772 (ptpt) REVERT: A 225 VAL cc_start: 0.7942 (t) cc_final: 0.7703 (t) REVERT: A 270 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6633 (pttm) REVERT: B 209 LYS cc_start: 0.8568 (mttm) cc_final: 0.7252 (mtmt) REVERT: B 268 ASN cc_start: 0.7557 (m110) cc_final: 0.7279 (m-40) REVERT: B 280 LYS cc_start: 0.8488 (tttp) cc_final: 0.8083 (mtpt) REVERT: E 83 MET cc_start: 0.6954 (mtm) cc_final: 0.6500 (mtm) REVERT: E 191 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7285 (mtt180) REVERT: R 140 LEU cc_start: 0.4615 (mp) cc_final: 0.4025 (mp) outliers start: 14 outliers final: 8 residues processed: 144 average time/residue: 0.2101 time to fit residues: 40.5036 Evaluate side-chains 150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138711 restraints weight = 10842.364| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.07 r_work: 0.3454 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8076 Z= 0.146 Angle : 0.499 7.445 11028 Z= 0.259 Chirality : 0.041 0.204 1324 Planarity : 0.003 0.038 1403 Dihedral : 4.811 75.542 1200 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.88 % Allowed : 20.73 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 1086 helix: 2.26 (0.30), residues: 350 sheet: 0.46 (0.33), residues: 252 loop : -1.57 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE E 29 TYR 0.012 0.001 TYR E 173 ARG 0.005 0.000 ARG E 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.782 Fit side-chains REVERT: A 197 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7761 (ptpt) REVERT: A 225 VAL cc_start: 0.7984 (t) cc_final: 0.7751 (t) REVERT: A 270 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6694 (pttm) REVERT: B 209 LYS cc_start: 0.8660 (mttm) cc_final: 0.7331 (mtmt) REVERT: B 268 ASN cc_start: 0.7582 (m110) cc_final: 0.7297 (m-40) REVERT: E 83 MET cc_start: 0.6975 (mtm) cc_final: 0.6494 (mtm) REVERT: R 126 PHE cc_start: 0.7016 (t80) cc_final: 0.6781 (t80) outliers start: 14 outliers final: 12 residues processed: 142 average time/residue: 0.2135 time to fit residues: 40.2451 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.167738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133970 restraints weight = 11046.343| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.07 r_work: 0.3418 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8076 Z= 0.308 Angle : 0.599 7.609 11028 Z= 0.313 Chirality : 0.045 0.220 1324 Planarity : 0.003 0.039 1403 Dihedral : 5.426 67.384 1200 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.88 % Allowed : 21.53 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1086 helix: 2.05 (0.30), residues: 348 sheet: 0.24 (0.33), residues: 259 loop : -1.65 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 211 HIS 0.006 0.001 HIS E 167 PHE 0.021 0.002 PHE B 234 TYR 0.016 0.002 TYR B 105 ARG 0.005 0.000 ARG E 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.46 seconds wall clock time: 91 minutes 58.09 seconds (5518.09 seconds total)