Starting phenix.real_space_refine on Tue Feb 11 19:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unn_42410/02_2025/8unn_42410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unn_42410/02_2025/8unn_42410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unn_42410/02_2025/8unn_42410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unn_42410/02_2025/8unn_42410.map" model { file = "/net/cci-nas-00/data/ceres_data/8unn_42410/02_2025/8unn_42410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unn_42410/02_2025/8unn_42410.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 C 4183 2.51 5 N 1122 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6503 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1690 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1678 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 231, 1678 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 1698 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2384 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 134 Chain: "G" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 338 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2043 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 133 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.51, per 1000 atoms: 0.85 Number of scatterers: 6503 At special positions: 0 Unit cell: (83.2992, 138.832, 98.9178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 3 15.00 O 1156 8.00 N 1122 7.00 C 4183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.877A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.786A pdb=" N GLN A 227 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 228 " --> pdb=" O GLY A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 228' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.574A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.884A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.071A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.674A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.678A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.536A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.118A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.583A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.709A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.519A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.540A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.777A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'R' and resid 121 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.987A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.628A pdb=" N ARG R 175 " --> pdb=" O HIS R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.719A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU R 187 " --> pdb=" O ASN R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.814A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.538A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.769A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 321 Processing helix chain 'R' and resid 322 through 327 Processing helix chain 'R' and resid 329 through 341 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.586A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.720A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.024A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.939A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.680A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.866A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.529A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1026 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: 1.57 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1369 1.33 - 1.45: 1613 1.45 - 1.57: 3608 1.57 - 1.69: 5 1.69 - 1.81: 53 Bond restraints: 6648 Sorted by residual: bond pdb=" CA GLN A 227 " pdb=" C GLN A 227 " ideal model delta sigma weight residual 1.522 1.442 0.081 1.43e-02 4.89e+03 3.20e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CA THR A 325 " pdb=" C THR A 325 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.22e-02 6.72e+03 1.41e+01 bond pdb=" N GLU A 230 " pdb=" CA GLU A 230 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.21e-02 6.83e+03 1.24e+01 ... (remaining 6643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 8988 2.40 - 4.81: 102 4.81 - 7.21: 21 7.21 - 9.61: 0 9.61 - 12.02: 3 Bond angle restraints: 9114 Sorted by residual: angle pdb=" N GLN G 11 " pdb=" CA GLN G 11 " pdb=" C GLN G 11 " ideal model delta sigma weight residual 111.28 99.26 12.02 1.09e+00 8.42e-01 1.22e+02 angle pdb=" C THR A 325 " pdb=" CA THR A 325 " pdb=" CB THR A 325 " ideal model delta sigma weight residual 110.17 102.99 7.18 1.11e+00 8.12e-01 4.19e+01 angle pdb=" N ASP B 5 " pdb=" CA ASP B 5 " pdb=" C ASP B 5 " ideal model delta sigma weight residual 111.28 105.50 5.78 1.09e+00 8.42e-01 2.82e+01 angle pdb=" N ALA B 11 " pdb=" CA ALA B 11 " pdb=" C ALA B 11 " ideal model delta sigma weight residual 111.28 117.01 -5.73 1.09e+00 8.42e-01 2.76e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" C GLN B 9 " ideal model delta sigma weight residual 111.28 106.25 5.03 1.09e+00 8.42e-01 2.13e+01 ... (remaining 9109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.22: 3758 33.22 - 66.43: 52 66.43 - 99.65: 2 99.65 - 132.87: 2 132.87 - 166.08: 3 Dihedral angle restraints: 3817 sinusoidal: 1185 harmonic: 2632 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -124.65 -166.08 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -59.70 164.30 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 291.08 142.41 148.67 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 3814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 681 0.030 - 0.060: 252 0.060 - 0.090: 100 0.090 - 0.120: 50 0.120 - 0.150: 11 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1091 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO G 49 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 226 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" C GLY A 226 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY A 226 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN A 227 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 222 " -0.012 2.00e-02 2.50e+03 1.22e-02 2.61e+00 pdb=" CG PHE A 222 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 222 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 222 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 222 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 222 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 222 " 0.001 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1049 2.76 - 3.29: 5980 3.29 - 3.83: 10224 3.83 - 4.36: 11087 4.36 - 4.90: 20550 Nonbonded interactions: 48890 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP A 295 " pdb=" N LEU A 296 " model vdw 2.319 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.328 3.040 nonbonded pdb=" OE1 GLN A 19 " pdb=" ND2 ASN B 88 " model vdw 2.342 3.120 ... (remaining 48885 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.930 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.005 0.089 6648 Z= 0.330 Angle : 0.672 12.017 9114 Z= 0.415 Chirality : 0.042 0.150 1094 Planarity : 0.004 0.081 1145 Dihedral : 13.918 166.085 2106 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 (0.28), residues: 888 helix: 2.27 (0.27), residues: 368 sheet: -0.06 (0.40), residues: 172 loop : -0.96 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 313 HIS 0.006 0.001 HIS R 296 PHE 0.026 0.001 PHE A 222 TYR 0.019 0.001 TYR B 59 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.677 Fit side-chains REVERT: R 272 LEU cc_start: 0.8446 (tp) cc_final: 0.8236 (tp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1516 time to fit residues: 20.0658 Evaluate side-chains 71 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN A 294 GLN R 178 HIS R 179 GLN R 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103774 restraints weight = 39006.205| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.71 r_work: 0.3065 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6648 Z= 0.196 Angle : 0.499 5.934 9114 Z= 0.272 Chirality : 0.041 0.150 1094 Planarity : 0.004 0.061 1145 Dihedral : 10.018 160.439 985 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.05 % Allowed : 7.69 % Favored : 91.26 % 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: 1.11 (0.28), residues: 888 helix: 2.37 (0.26), residues: 390 sheet: -0.02 (0.40), residues: 172 loop : -0.87 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.010 0.001 HIS A 220 PHE 0.031 0.001 PHE A 222 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.675 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.1359 time to fit residues: 16.3376 Evaluate side-chains 75 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 264 ASN A 294 GLN B 183 HIS B 259 GLN R 178 HIS R 296 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105244 restraints weight = 43413.421| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 4.79 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6648 Z= 0.145 Angle : 0.454 6.208 9114 Z= 0.245 Chirality : 0.040 0.149 1094 Planarity : 0.003 0.057 1145 Dihedral : 9.405 164.695 985 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.70 % Allowed : 11.36 % Favored : 87.94 % 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: 1.29 (0.29), residues: 888 helix: 2.48 (0.27), residues: 393 sheet: 0.10 (0.40), residues: 171 loop : -0.77 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.013 0.001 HIS A 220 PHE 0.029 0.001 PHE A 222 TYR 0.010 0.001 TYR A 358 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.791 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.1471 time to fit residues: 17.3348 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 294 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102626 restraints weight = 35915.610| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.49 r_work: 0.3055 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6648 Z= 0.187 Angle : 0.468 6.677 9114 Z= 0.252 Chirality : 0.041 0.149 1094 Planarity : 0.003 0.053 1145 Dihedral : 9.117 170.516 985 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.75 % Allowed : 13.46 % Favored : 84.79 % 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: 1.17 (0.29), residues: 888 helix: 2.36 (0.27), residues: 403 sheet: -0.06 (0.40), residues: 172 loop : -0.86 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.010 0.001 HIS A 220 PHE 0.019 0.001 PHE A 222 TYR 0.010 0.001 TYR A 358 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.717 Fit side-chains REVERT: A 294 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8762 (tp40) REVERT: R 192 ASP cc_start: 0.8149 (m-30) cc_final: 0.7912 (m-30) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.1473 time to fit residues: 18.1300 Evaluate side-chains 76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 236 GLN R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104443 restraints weight = 32516.673| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.30 r_work: 0.3095 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6648 Z= 0.146 Angle : 0.442 6.647 9114 Z= 0.239 Chirality : 0.040 0.145 1094 Planarity : 0.003 0.056 1145 Dihedral : 9.060 177.013 985 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.62 % Allowed : 12.94 % Favored : 84.44 % 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: 1.25 (0.29), residues: 888 helix: 2.50 (0.27), residues: 398 sheet: -0.03 (0.40), residues: 171 loop : -0.86 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.010 0.001 HIS A 220 PHE 0.009 0.001 PHE B 199 TYR 0.007 0.001 TYR R 308 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.781 Fit side-chains REVERT: A 23 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7952 (t0) REVERT: A 53 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7773 (mtmm) REVERT: A 294 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8748 (tp40) REVERT: R 192 ASP cc_start: 0.7857 (m-30) cc_final: 0.7619 (m-30) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 0.1468 time to fit residues: 18.1668 Evaluate side-chains 83 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102734 restraints weight = 38233.122| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.66 r_work: 0.3056 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6648 Z= 0.196 Angle : 0.463 6.663 9114 Z= 0.249 Chirality : 0.041 0.149 1094 Planarity : 0.003 0.058 1145 Dihedral : 9.106 179.913 985 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.27 % Allowed : 14.34 % Favored : 83.39 % 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: 1.13 (0.29), residues: 888 helix: 2.45 (0.27), residues: 397 sheet: -0.24 (0.39), residues: 172 loop : -0.87 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 211 HIS 0.010 0.001 HIS A 220 PHE 0.012 0.001 PHE A 222 TYR 0.009 0.001 TYR B 289 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.746 Fit side-chains REVERT: A 53 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7779 (mtmm) REVERT: A 294 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8793 (tp40) REVERT: B 45 MET cc_start: 0.8631 (mmt) cc_final: 0.8015 (mmt) REVERT: R 192 ASP cc_start: 0.7993 (m-30) cc_final: 0.7758 (m-30) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.1424 time to fit residues: 16.6652 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 236 GLN R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101972 restraints weight = 46182.963| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.69 r_work: 0.3004 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6648 Z= 0.255 Angle : 0.494 6.599 9114 Z= 0.268 Chirality : 0.042 0.155 1094 Planarity : 0.003 0.060 1145 Dihedral : 9.175 178.688 985 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.97 % Allowed : 13.29 % Favored : 83.74 % 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: 1.02 (0.29), residues: 888 helix: 2.38 (0.27), residues: 397 sheet: -0.40 (0.39), residues: 172 loop : -0.91 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.013 0.001 HIS A 220 PHE 0.010 0.001 PHE B 235 TYR 0.010 0.001 TYR A 339 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.702 Fit side-chains REVERT: A 53 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7869 (mtmm) REVERT: A 294 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8857 (tp40) REVERT: R 192 ASP cc_start: 0.8197 (m-30) cc_final: 0.7985 (m-30) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.1446 time to fit residues: 17.4463 Evaluate side-chains 78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103943 restraints weight = 37001.702| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.40 r_work: 0.3071 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6648 Z= 0.153 Angle : 0.447 6.493 9114 Z= 0.242 Chirality : 0.040 0.142 1094 Planarity : 0.003 0.058 1145 Dihedral : 8.955 173.682 985 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.45 % Allowed : 14.16 % Favored : 83.39 % 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: 1.11 (0.29), residues: 888 helix: 2.36 (0.27), residues: 403 sheet: -0.34 (0.40), residues: 172 loop : -0.80 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.014 0.001 HIS A 220 PHE 0.021 0.001 PHE R 49 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.694 Fit side-chains REVERT: A 53 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7800 (mtmm) REVERT: A 294 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8775 (tp40) REVERT: R 192 ASP cc_start: 0.8079 (m-30) cc_final: 0.7859 (m-30) outliers start: 14 outliers final: 12 residues processed: 85 average time/residue: 0.1407 time to fit residues: 17.5088 Evaluate side-chains 80 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104737 restraints weight = 43924.736| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.82 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6648 Z= 0.164 Angle : 0.455 6.480 9114 Z= 0.247 Chirality : 0.040 0.143 1094 Planarity : 0.003 0.058 1145 Dihedral : 8.888 170.725 985 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.62 % Allowed : 14.16 % Favored : 83.22 % 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: 1.10 (0.29), residues: 888 helix: 2.40 (0.27), residues: 399 sheet: -0.37 (0.40), residues: 172 loop : -0.82 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.018 0.001 HIS A 220 PHE 0.018 0.001 PHE R 49 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.676 Fit side-chains REVERT: B 45 MET cc_start: 0.8523 (mmt) cc_final: 0.7926 (mmt) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.1465 time to fit residues: 17.7727 Evaluate side-chains 78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101726 restraints weight = 33345.360| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.96 r_work: 0.3023 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6648 Z= 0.327 Angle : 0.543 6.216 9114 Z= 0.296 Chirality : 0.043 0.156 1094 Planarity : 0.004 0.060 1145 Dihedral : 9.004 167.359 985 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 14.51 % Favored : 83.04 % 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: 0.80 (0.29), residues: 888 helix: 2.17 (0.27), residues: 399 sheet: -0.56 (0.40), residues: 172 loop : -0.97 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 99 HIS 0.024 0.002 HIS A 220 PHE 0.017 0.002 PHE R 49 TYR 0.013 0.002 TYR B 289 ARG 0.004 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.657 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1408 time to fit residues: 16.8795 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104643 restraints weight = 42129.116| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.68 r_work: 0.3061 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6648 Z= 0.162 Angle : 0.466 6.238 9114 Z= 0.255 Chirality : 0.040 0.143 1094 Planarity : 0.003 0.058 1145 Dihedral : 8.737 164.277 985 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.10 % Allowed : 15.21 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 888 helix: 2.27 (0.27), residues: 403 sheet: -0.46 (0.41), residues: 172 loop : -0.87 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 99 HIS 0.021 0.001 HIS A 220 PHE 0.018 0.001 PHE R 49 TYR 0.011 0.001 TYR A 358 ARG 0.004 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3150.32 seconds wall clock time: 56 minutes 24.19 seconds (3384.19 seconds total)