Starting phenix.real_space_refine on Thu Jul 2 21:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyx_26197/07_2026/7tyx_26197.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.098 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 71 5.16 5 C 6565 2.51 5 N 1739 2.21 5 O 1844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10219 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 804 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASP:plan': 6, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "P" Number of atoms: 284 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Conformer: "B" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 265 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2962 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1909 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 256 Unusual residues: {'NAG': 3, 'PLM': 8, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG P 18 " occ=0.50 Time building chain proxies: 2.10, per 1000 atoms: 0.21 Number of scatterers: 10219 At special positions: 0 Unit cell: (125.33, 107.07, 141.93, 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 71 16.00 O 1844 8.00 N 1739 7.00 C 6565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 125 " " NAG R 502 " - " ASN R 130 " " NAG R 503 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 290.2 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 45.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.583A pdb=" N ALA E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.342A pdb=" N CYS E 84 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 107 removed outlier: 5.670A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Proline residue: E 92 - end of helix Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.784A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 3.791A pdb=" N ALA E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Proline residue: E 153 - end of helix removed outlier: 3.580A pdb=" N LEU E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 40 through 61 Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.245A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.931A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.553A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.851A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.063A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.510A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.652A pdb=" N LEU R 291 " --> pdb=" O ASN R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 331 Proline residue: R 304 - end of helix removed outlier: 3.600A pdb=" N ASN R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.569A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.576A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.502A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.899A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.573A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.273A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.536A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.581A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.540A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.676A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.713A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 removed outlier: 3.769A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.818A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.237A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.522A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.663A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.907A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.584A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.567A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.544A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.861A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1486 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: 1.43 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1637 1.32 - 1.44: 2928 1.44 - 1.57: 5793 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 10457 Sorted by residual: bond pdb=" N GLY P 33 " pdb=" CA GLY P 33 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.06e-02 8.90e+03 8.03e+00 bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N ASN P 35 " pdb=" CA ASN P 35 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 bond pdb=" N SER P 34 " pdb=" CA SER P 34 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.86e+00 ... (remaining 10452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 13631 1.20 - 2.40: 436 2.40 - 3.60: 82 3.60 - 4.79: 9 4.79 - 5.99: 10 Bond angle restraints: 14168 Sorted by residual: angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 122.28 118.37 3.91 1.00e+00 1.00e+00 1.52e+01 angle pdb=" CA THR P 36 " pdb=" C THR P 36 " pdb=" O THR P 36 " ideal model delta sigma weight residual 121.55 117.78 3.77 1.06e+00 8.90e-01 1.27e+01 angle pdb=" C GLU R 255 " pdb=" N LYS R 256 " pdb=" CA LYS R 256 " ideal model delta sigma weight residual 121.87 127.54 -5.67 2.24e+00 1.99e-01 6.42e+00 angle pdb=" C ASN R 124 " pdb=" N ASN R 125 " pdb=" CA ASN R 125 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.40e+00 angle pdb=" CA ASN P 35 " pdb=" C ASN P 35 " pdb=" O ASN P 35 " ideal model delta sigma weight residual 120.55 117.99 2.56 1.06e+00 8.90e-01 5.82e+00 ... (remaining 14163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5693 17.83 - 35.67: 376 35.67 - 53.50: 83 53.50 - 71.33: 23 71.33 - 89.16: 9 Dihedral angle restraints: 6184 sinusoidal: 2469 harmonic: 3715 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 177.67 -84.67 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -48.61 -37.39 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1438 0.069 - 0.137: 128 0.137 - 0.206: 4 0.206 - 0.274: 1 0.274 - 0.343: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 125 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1569 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 304 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 91 " -0.021 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 92 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 92 " -0.018 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1833 2.76 - 3.30: 9357 3.30 - 3.83: 16551 3.83 - 4.37: 21526 4.37 - 4.90: 35885 Nonbonded interactions: 85152 Sorted by model distance: nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.231 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.261 3.040 nonbonded pdb=" O ILE R 347 " pdb=" OH TYR R 391 " model vdw 2.267 3.040 nonbonded pdb=" O GLU R 397 " pdb=" OG1 THR R 401 " model vdw 2.268 3.040 nonbonded pdb=" O LEU R 62 " pdb=" NH2 ARG R 74 " model vdw 2.269 3.120 ... (remaining 85147 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10470 Z= 0.209 Angle : 0.531 10.281 14195 Z= 0.301 Chirality : 0.041 0.343 1572 Planarity : 0.003 0.039 1785 Dihedral : 13.237 89.163 3753 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.62 % Allowed : 11.62 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.19), residues: 1252 helix: -3.28 (0.13), residues: 518 sheet: -0.41 (0.31), residues: 229 loop : -1.30 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.009 0.001 TYR R 391 PHE 0.011 0.001 PHE A 212 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (10457) covalent geometry : angle 0.51797 / 0.30 (14168) SS BOND : bond 0.00300 / 0.20 ( 9) SS BOND : angle 0.83813 / 0.49 ( 18) hydrogen bonds : bond 0.26453 / 18.19 ( 518) hydrogen bonds : angle 9.01964 / 6.50 ( 1486) Misc. bond : bond 0.10626 / 5.59 ( 1) link_NAG-ASN : bond 0.00937 / 0.45 ( 3) link_NAG-ASN : angle 4.63061 / 2.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.280 Fit side-chains REVERT: R 101 ASP cc_start: 0.5997 (m-30) cc_final: 0.5636 (m-30) REVERT: R 143 LYS cc_start: 0.7668 (tttt) cc_final: 0.7401 (ttpp) REVERT: A 311 TYR cc_start: 0.2458 (m-80) cc_final: 0.2258 (m-80) REVERT: A 368 ASP cc_start: 0.7438 (m-30) cc_final: 0.6859 (m-30) REVERT: A 386 MET cc_start: 0.6756 (ttm) cc_final: 0.6375 (mtt) REVERT: A 389 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7355 (ttm110) REVERT: A 390 GLN cc_start: 0.7358 (mt0) cc_final: 0.7065 (mp10) REVERT: B 17 GLN cc_start: 0.6387 (tt0) cc_final: 0.6143 (tm-30) outliers start: 17 outliers final: 2 residues processed: 212 average time/residue: 0.4370 time to fit residues: 100.3782 Evaluate side-chains 138 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain A residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 14 ASN P 22 ASN P 35 ASN R 52 GLN R 135 ASN R 184 HIS R 186 ASN R 227 GLN R 395 ASN R 399 GLN A 14 ASN A 292 ASN B 17 GLN N 3 GLN N 35 ASN N 39 GLN N 120 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.216725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155089 restraints weight = 24204.403| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.62 r_work: 0.3708 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10470 Z= 0.145 Angle : 0.584 9.552 14195 Z= 0.305 Chirality : 0.043 0.294 1572 Planarity : 0.004 0.049 1785 Dihedral : 5.537 59.245 1522 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.14 % Allowed : 16.19 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1252 helix: 0.01 (0.21), residues: 514 sheet: -0.13 (0.31), residues: 245 loop : -0.84 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 347 TYR 0.021 0.001 TYR N 60 PHE 0.016 0.002 PHE A 212 TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS R 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10457) covalent geometry : angle 0.57401 / 0.30 (14168) SS BOND : bond 0.00217 / 0.12 ( 9) SS BOND : angle 1.01495 / 0.56 ( 18) hydrogen bonds : bond 0.05111 / 3.47 ( 518) hydrogen bonds : angle 5.08533 / 3.73 ( 1486) Misc. bond : bond 0.00037 / 0.02 ( 1) link_NAG-ASN : bond 0.00947 / 0.45 ( 3) link_NAG-ASN : angle 4.07660 / 2.37 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: R 101 ASP cc_start: 0.5226 (m-30) cc_final: 0.4959 (m-30) REVERT: R 140 GLU cc_start: 0.6471 (tp30) cc_final: 0.5987 (tp30) REVERT: R 143 LYS cc_start: 0.6563 (tttt) cc_final: 0.6311 (ttpp) REVERT: R 174 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6482 (mtt180) REVERT: R 187 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5664 (tpt) REVERT: R 237 MET cc_start: 0.7365 (mtt) cc_final: 0.7165 (mtt) REVERT: R 346 MET cc_start: 0.6707 (mmt) cc_final: 0.6478 (mmp) REVERT: R 405 GLN cc_start: 0.6887 (mp10) cc_final: 0.6567 (mp10) REVERT: A 311 TYR cc_start: 0.2619 (m-80) cc_final: 0.2124 (m-80) REVERT: A 386 MET cc_start: 0.6072 (ttm) cc_final: 0.5383 (mtt) REVERT: A 389 ARG cc_start: 0.7606 (ttt90) cc_final: 0.6315 (ttm110) REVERT: A 390 GLN cc_start: 0.6295 (mt0) cc_final: 0.5694 (mp10) REVERT: B 17 GLN cc_start: 0.5808 (tt0) cc_final: 0.5548 (tm-30) REVERT: B 59 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7315 (t80) REVERT: B 195 ASP cc_start: 0.7278 (p0) cc_final: 0.6868 (p0) REVERT: B 217 MET cc_start: 0.7301 (ptt) cc_final: 0.6934 (pmt) REVERT: N 25 SER cc_start: 0.6116 (OUTLIER) cc_final: 0.5429 (t) REVERT: N 60 TYR cc_start: 0.7019 (m-80) cc_final: 0.6725 (m-80) outliers start: 33 outliers final: 12 residues processed: 172 average time/residue: 0.5197 time to fit residues: 96.6597 Evaluate side-chains 149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 66 optimal weight: 40.0000 chunk 8 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 ASN A 357 HIS B 220 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.215984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153901 restraints weight = 27228.692| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.78 r_work: 0.3702 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10470 Z= 0.133 Angle : 0.536 9.153 14195 Z= 0.280 Chirality : 0.042 0.286 1572 Planarity : 0.004 0.053 1785 Dihedral : 5.197 55.543 1520 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.62 % Allowed : 16.00 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1252 helix: 1.14 (0.23), residues: 515 sheet: -0.13 (0.31), residues: 250 loop : -0.69 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.015 0.001 TYR N 60 PHE 0.015 0.001 PHE A 212 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10457) covalent geometry : angle 0.52521 / 0.28 (14168) SS BOND : bond 0.00343 / 0.23 ( 9) SS BOND : angle 1.17870 / 0.68 ( 18) hydrogen bonds : bond 0.04480 / 3.02 ( 518) hydrogen bonds : angle 4.71305 / 3.45 ( 1486) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00910 / 0.43 ( 3) link_NAG-ASN : angle 3.93899 / 2.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6184 (p) REVERT: E 167 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5722 (ttm110) REVERT: R 101 ASP cc_start: 0.5343 (m-30) cc_final: 0.5106 (m-30) REVERT: R 140 GLU cc_start: 0.6474 (tp30) cc_final: 0.5980 (tp30) REVERT: R 143 LYS cc_start: 0.6500 (tttt) cc_final: 0.6257 (ttpp) REVERT: R 174 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6626 (mtt180) REVERT: R 187 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6162 (tpt) REVERT: R 405 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6331 (mp10) REVERT: A 60 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5488 (mpp) REVERT: A 356 ARG cc_start: 0.7107 (ptt-90) cc_final: 0.6550 (ptt-90) REVERT: A 386 MET cc_start: 0.5999 (ttm) cc_final: 0.5525 (mtp) REVERT: A 389 ARG cc_start: 0.7610 (ttt90) cc_final: 0.6335 (ttm110) REVERT: A 390 GLN cc_start: 0.6405 (mt0) cc_final: 0.5799 (mp10) REVERT: B 13 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6741 (mm-40) REVERT: B 17 GLN cc_start: 0.5839 (tt0) cc_final: 0.5633 (tm-30) REVERT: B 59 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7120 (t80) REVERT: B 154 ASP cc_start: 0.7413 (m-30) cc_final: 0.7188 (m-30) REVERT: B 173 THR cc_start: 0.6631 (m) cc_final: 0.6223 (p) REVERT: B 217 MET cc_start: 0.7305 (ptt) cc_final: 0.6909 (pmt) REVERT: N 1 GLN cc_start: 0.6477 (tp-100) cc_final: 0.6275 (tp40) REVERT: N 5 GLN cc_start: 0.7088 (tt0) cc_final: 0.6539 (mt0) REVERT: N 25 SER cc_start: 0.6148 (OUTLIER) cc_final: 0.5593 (t) REVERT: N 60 TYR cc_start: 0.7043 (m-80) cc_final: 0.6771 (m-80) outliers start: 38 outliers final: 14 residues processed: 164 average time/residue: 0.4723 time to fit residues: 83.8884 Evaluate side-chains 154 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 124 HIS P 10 GLN R 121 HIS B 175 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.208289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145840 restraints weight = 24649.134| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.60 r_work: 0.3624 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10470 Z= 0.252 Angle : 0.677 10.285 14195 Z= 0.349 Chirality : 0.048 0.285 1572 Planarity : 0.005 0.058 1785 Dihedral : 6.309 49.446 1520 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.57 % Allowed : 15.62 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.23), residues: 1252 helix: 1.14 (0.23), residues: 515 sheet: -0.50 (0.31), residues: 254 loop : -0.76 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 356 TYR 0.016 0.002 TYR R 391 PHE 0.022 0.003 PHE A 345 TRP 0.016 0.002 TRP B 82 HIS 0.008 0.002 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (10457) covalent geometry : angle 0.66932 / 0.35 (14168) SS BOND : bond 0.00313 / 0.19 ( 9) SS BOND : angle 1.18084 / 0.68 ( 18) hydrogen bonds : bond 0.05370 / 3.66 ( 518) hydrogen bonds : angle 5.05660 / 3.70 ( 1486) Misc. bond : bond 0.00027 / 0.01 ( 1) link_NAG-ASN : bond 0.00877 / 0.42 ( 3) link_NAG-ASN : angle 3.72888 / 2.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.337 Fit side-chains REVERT: E 99 CYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6311 (p) REVERT: R 101 ASP cc_start: 0.5527 (m-30) cc_final: 0.5294 (m-30) REVERT: R 105 SER cc_start: 0.7877 (m) cc_final: 0.7660 (p) REVERT: R 140 GLU cc_start: 0.6508 (tp30) cc_final: 0.6035 (tp30) REVERT: R 210 GLU cc_start: 0.6291 (tm-30) cc_final: 0.6044 (tm-30) REVERT: R 257 GLN cc_start: 0.7041 (mt0) cc_final: 0.6614 (mt0) REVERT: R 287 ASP cc_start: 0.6466 (t0) cc_final: 0.6164 (t0) REVERT: R 328 ARG cc_start: 0.6279 (mtt180) cc_final: 0.5772 (mtm-85) REVERT: R 367 MET cc_start: 0.3802 (OUTLIER) cc_final: 0.3597 (ttt) REVERT: R 405 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.6114 (mp10) REVERT: A 28 LYS cc_start: 0.6705 (pptt) cc_final: 0.5917 (ptpt) REVERT: A 31 GLN cc_start: 0.6124 (mm110) cc_final: 0.5840 (mm110) REVERT: A 35 GLN cc_start: 0.6384 (tt0) cc_final: 0.5526 (mp-120) REVERT: A 389 ARG cc_start: 0.7582 (ttt90) cc_final: 0.6343 (ttm110) REVERT: A 390 GLN cc_start: 0.6305 (mt0) cc_final: 0.5670 (mp10) REVERT: B 4 LEU cc_start: 0.3873 (OUTLIER) cc_final: 0.3611 (tp) REVERT: B 13 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6400 (tm-30) REVERT: B 59 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 215 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7294 (mm-30) REVERT: B 217 MET cc_start: 0.7259 (ptt) cc_final: 0.6574 (pmm) REVERT: N 25 SER cc_start: 0.6438 (OUTLIER) cc_final: 0.5913 (t) REVERT: N 34 MET cc_start: 0.7611 (mmm) cc_final: 0.7345 (mmm) REVERT: N 57 SER cc_start: 0.7153 (m) cc_final: 0.6861 (t) REVERT: N 60 TYR cc_start: 0.7161 (m-80) cc_final: 0.6828 (m-80) REVERT: N 108 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7359 (m-80) outliers start: 48 outliers final: 21 residues processed: 177 average time/residue: 0.5123 time to fit residues: 97.6674 Evaluate side-chains 163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 10.0000 chunk 118 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN R 201 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.213023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151328 restraints weight = 22799.662| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.50 r_work: 0.3688 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10470 Z= 0.125 Angle : 0.528 8.847 14195 Z= 0.276 Chirality : 0.042 0.285 1572 Planarity : 0.004 0.058 1785 Dihedral : 5.775 51.374 1520 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.86 % Allowed : 17.43 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1252 helix: 1.65 (0.23), residues: 516 sheet: -0.33 (0.32), residues: 247 loop : -0.60 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.017 0.001 TYR N 60 PHE 0.015 0.001 PHE A 212 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10457) covalent geometry : angle 0.51914 / 0.27 (14168) SS BOND : bond 0.00418 / 0.31 ( 9) SS BOND : angle 0.90265 / 0.50 ( 18) hydrogen bonds : bond 0.04070 / 2.77 ( 518) hydrogen bonds : angle 4.65243 / 3.40 ( 1486) Misc. bond : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : bond 0.00871 / 0.41 ( 3) link_NAG-ASN : angle 3.61107 / 2.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.411 Fit side-chains REVERT: E 99 CYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6276 (p) REVERT: R 140 GLU cc_start: 0.6699 (tp30) cc_final: 0.6362 (tp30) REVERT: R 210 GLU cc_start: 0.6353 (tm-30) cc_final: 0.6123 (tm-30) REVERT: R 257 GLN cc_start: 0.7060 (mt0) cc_final: 0.6572 (mt0) REVERT: R 287 ASP cc_start: 0.6326 (t0) cc_final: 0.6039 (t0) REVERT: R 367 MET cc_start: 0.3740 (OUTLIER) cc_final: 0.3481 (ttt) REVERT: R 405 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6307 (mp10) REVERT: A 28 LYS cc_start: 0.6711 (pptt) cc_final: 0.5962 (ptpt) REVERT: A 31 GLN cc_start: 0.5980 (mm110) cc_final: 0.5726 (mm110) REVERT: A 35 GLN cc_start: 0.6295 (tt0) cc_final: 0.5424 (mp-120) REVERT: A 389 ARG cc_start: 0.7591 (ttt90) cc_final: 0.6349 (ttm110) REVERT: A 390 GLN cc_start: 0.6315 (mt0) cc_final: 0.5681 (mp10) REVERT: B 4 LEU cc_start: 0.4069 (OUTLIER) cc_final: 0.3827 (tp) REVERT: B 13 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6511 (tm-30) REVERT: B 215 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7377 (mm-30) REVERT: B 217 MET cc_start: 0.7244 (ptt) cc_final: 0.6685 (pmt) REVERT: N 25 SER cc_start: 0.6448 (OUTLIER) cc_final: 0.5867 (t) REVERT: N 34 MET cc_start: 0.7575 (mmm) cc_final: 0.7326 (mmm) REVERT: N 43 LYS cc_start: 0.6730 (mtpt) cc_final: 0.6519 (mttt) REVERT: N 60 TYR cc_start: 0.7054 (m-80) cc_final: 0.6787 (m-80) REVERT: N 105 ARG cc_start: 0.6695 (mtp180) cc_final: 0.6298 (mtp180) outliers start: 30 outliers final: 15 residues processed: 158 average time/residue: 0.5167 time to fit residues: 88.2223 Evaluate side-chains 153 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 30.0000 chunk 107 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.214983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153351 restraints weight = 23817.051| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.58 r_work: 0.3707 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10470 Z= 0.109 Angle : 0.502 8.775 14195 Z= 0.260 Chirality : 0.041 0.288 1572 Planarity : 0.004 0.058 1785 Dihedral : 5.407 52.672 1520 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.43 % Allowed : 17.52 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1252 helix: 1.95 (0.23), residues: 518 sheet: -0.31 (0.32), residues: 248 loop : -0.48 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.017 0.001 TYR N 60 PHE 0.015 0.001 PHE R 99 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (10457) covalent geometry : angle 0.49378 / 0.26 (14168) SS BOND : bond 0.00207 / 0.13 ( 9) SS BOND : angle 0.69987 / 0.39 ( 18) hydrogen bonds : bond 0.03694 / 2.50 ( 518) hydrogen bonds : angle 4.41813 / 3.24 ( 1486) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00864 / 0.41 ( 3) link_NAG-ASN : angle 3.50928 / 2.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.395 Fit side-chains REVERT: E 99 CYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6284 (p) REVERT: E 167 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5936 (ttm110) REVERT: P 16 LEU cc_start: 0.5996 (mt) cc_final: 0.5791 (mm) REVERT: R 106 GLU cc_start: 0.5573 (mm-30) cc_final: 0.5335 (mm-30) REVERT: R 187 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.5814 (tpt) REVERT: R 210 GLU cc_start: 0.6375 (tm-30) cc_final: 0.6151 (tm-30) REVERT: R 257 GLN cc_start: 0.7084 (mt0) cc_final: 0.6800 (mt0) REVERT: R 287 ASP cc_start: 0.6320 (t0) cc_final: 0.5988 (t0) REVERT: R 288 ASN cc_start: 0.6820 (m-40) cc_final: 0.6272 (m-40) REVERT: R 367 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.3436 (ttt) REVERT: R 405 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6302 (mp10) REVERT: A 28 LYS cc_start: 0.6827 (pptt) cc_final: 0.6184 (ptpt) REVERT: A 31 GLN cc_start: 0.5970 (mm110) cc_final: 0.5738 (mm110) REVERT: A 35 GLN cc_start: 0.6265 (tt0) cc_final: 0.5412 (mp-120) REVERT: A 60 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5581 (mpp) REVERT: A 389 ARG cc_start: 0.7571 (ttt90) cc_final: 0.6289 (ttm110) REVERT: A 390 GLN cc_start: 0.6322 (mt0) cc_final: 0.5650 (mp10) REVERT: B 4 LEU cc_start: 0.4083 (OUTLIER) cc_final: 0.3845 (tp) REVERT: B 13 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6520 (tm-30) REVERT: B 215 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7297 (mp0) REVERT: B 217 MET cc_start: 0.7265 (ptt) cc_final: 0.6674 (pmm) REVERT: N 5 GLN cc_start: 0.7180 (tt0) cc_final: 0.6331 (tm-30) REVERT: N 43 LYS cc_start: 0.6714 (mtpt) cc_final: 0.6496 (mttt) REVERT: N 60 TYR cc_start: 0.6970 (m-80) cc_final: 0.6752 (m-80) REVERT: N 105 ARG cc_start: 0.6711 (mtp180) cc_final: 0.6350 (mtm-85) REVERT: N 108 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7247 (m-80) outliers start: 36 outliers final: 15 residues processed: 167 average time/residue: 0.4973 time to fit residues: 89.8717 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 53 optimal weight: 0.0010 chunk 54 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.216917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156222 restraints weight = 22517.778| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.50 r_work: 0.3740 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10470 Z= 0.095 Angle : 0.486 8.747 14195 Z= 0.253 Chirality : 0.041 0.290 1572 Planarity : 0.003 0.057 1785 Dihedral : 5.191 54.524 1520 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.67 % Allowed : 18.57 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1252 helix: 2.19 (0.23), residues: 518 sheet: -0.25 (0.32), residues: 248 loop : -0.39 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.017 0.001 TYR N 60 PHE 0.016 0.001 PHE R 99 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (10457) covalent geometry : angle 0.47721 / 0.25 (14168) SS BOND : bond 0.00189 / 0.12 ( 9) SS BOND : angle 1.04117 / 0.46 ( 18) hydrogen bonds : bond 0.03378 / 2.28 ( 518) hydrogen bonds : angle 4.27018 / 3.13 ( 1486) Misc. bond : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : bond 0.00862 / 0.41 ( 3) link_NAG-ASN : angle 3.44415 / 2.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6219 (p) REVERT: E 167 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5820 (ttm110) REVERT: R 187 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5701 (tpt) REVERT: R 257 GLN cc_start: 0.7035 (mt0) cc_final: 0.6792 (mt0) REVERT: R 287 ASP cc_start: 0.6246 (t0) cc_final: 0.5986 (t0) REVERT: R 288 ASN cc_start: 0.6549 (m-40) cc_final: 0.6107 (m-40) REVERT: R 367 MET cc_start: 0.3705 (OUTLIER) cc_final: 0.3413 (ttt) REVERT: R 382 PHE cc_start: 0.6812 (m-80) cc_final: 0.6503 (m-80) REVERT: R 405 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6246 (mp10) REVERT: A 28 LYS cc_start: 0.6813 (pptt) cc_final: 0.6188 (ptpt) REVERT: A 31 GLN cc_start: 0.6019 (mm110) cc_final: 0.5789 (mm110) REVERT: A 35 GLN cc_start: 0.6248 (tt0) cc_final: 0.5373 (mp-120) REVERT: A 389 ARG cc_start: 0.7515 (ttt90) cc_final: 0.6281 (ttm110) REVERT: A 390 GLN cc_start: 0.6376 (mt0) cc_final: 0.5723 (mp10) REVERT: B 13 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6605 (tm-30) REVERT: B 195 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7064 (p0) REVERT: B 215 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7294 (mp0) REVERT: B 217 MET cc_start: 0.7273 (ptt) cc_final: 0.6700 (pmm) REVERT: N 5 GLN cc_start: 0.7168 (tt0) cc_final: 0.6302 (tm-30) REVERT: N 108 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7008 (m-80) outliers start: 28 outliers final: 14 residues processed: 168 average time/residue: 0.4609 time to fit residues: 84.0548 Evaluate side-chains 160 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 111 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 103 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.212542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151429 restraints weight = 21143.014| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.33 r_work: 0.3688 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10470 Z= 0.167 Angle : 0.553 8.754 14195 Z= 0.286 Chirality : 0.044 0.294 1572 Planarity : 0.004 0.058 1785 Dihedral : 5.579 51.444 1520 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.05 % Allowed : 18.38 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1252 helix: 2.00 (0.23), residues: 519 sheet: -0.29 (0.32), residues: 250 loop : -0.44 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.022 0.001 TYR N 60 PHE 0.017 0.002 PHE R 99 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (10457) covalent geometry : angle 0.54500 / 0.28 (14168) SS BOND : bond 0.00280 / 0.18 ( 9) SS BOND : angle 1.05381 / 0.50 ( 18) hydrogen bonds : bond 0.04127 / 2.80 ( 518) hydrogen bonds : angle 4.48713 / 3.29 ( 1486) Misc. bond : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : bond 0.00849 / 0.40 ( 3) link_NAG-ASN : angle 3.44840 / 2.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.375 Fit side-chains REVERT: E 99 CYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6345 (p) REVERT: R 187 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6243 (tpt) REVERT: R 257 GLN cc_start: 0.7117 (mt0) cc_final: 0.6865 (mt0) REVERT: R 287 ASP cc_start: 0.6264 (t0) cc_final: 0.5966 (t0) REVERT: R 288 ASN cc_start: 0.6605 (m-40) cc_final: 0.6126 (m-40) REVERT: R 367 MET cc_start: 0.3692 (OUTLIER) cc_final: 0.3417 (ttt) REVERT: R 405 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6162 (mp10) REVERT: A 31 GLN cc_start: 0.6119 (mm110) cc_final: 0.5880 (mm110) REVERT: A 35 GLN cc_start: 0.6379 (tt0) cc_final: 0.5454 (mp-120) REVERT: A 253 TYR cc_start: 0.5382 (p90) cc_final: 0.5167 (p90) REVERT: A 389 ARG cc_start: 0.7535 (ttt90) cc_final: 0.6285 (ttm110) REVERT: A 390 GLN cc_start: 0.6365 (mt0) cc_final: 0.5698 (mp10) REVERT: B 4 LEU cc_start: 0.4081 (OUTLIER) cc_final: 0.3850 (tp) REVERT: B 13 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6566 (tm-30) REVERT: B 59 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7310 (t80) REVERT: B 195 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7074 (p0) REVERT: B 215 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7318 (mp0) REVERT: B 217 MET cc_start: 0.7275 (ptt) cc_final: 0.6621 (pmm) REVERT: N 5 GLN cc_start: 0.7212 (tt0) cc_final: 0.6487 (mt0) REVERT: N 25 SER cc_start: 0.6500 (OUTLIER) cc_final: 0.5923 (t) REVERT: N 43 LYS cc_start: 0.6514 (mtpt) cc_final: 0.6228 (mttt) REVERT: N 108 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7254 (m-80) outliers start: 32 outliers final: 19 residues processed: 153 average time/residue: 0.4887 time to fit residues: 81.1672 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.214264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154510 restraints weight = 16024.939| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.99 r_work: 0.3727 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10470 Z= 0.118 Angle : 0.524 10.075 14195 Z= 0.271 Chirality : 0.042 0.295 1572 Planarity : 0.003 0.058 1785 Dihedral : 5.486 51.781 1520 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.86 % Allowed : 18.67 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1252 helix: 2.12 (0.23), residues: 517 sheet: -0.30 (0.32), residues: 251 loop : -0.40 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.022 0.001 TYR N 60 PHE 0.017 0.001 PHE R 99 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10457) covalent geometry : angle 0.51649 / 0.27 (14168) SS BOND : bond 0.00240 / 0.16 ( 9) SS BOND : angle 0.88192 / 0.45 ( 18) hydrogen bonds : bond 0.03752 / 2.54 ( 518) hydrogen bonds : angle 4.37786 / 3.21 ( 1486) Misc. bond : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : bond 0.00858 / 0.41 ( 3) link_NAG-ASN : angle 3.37664 / 1.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6378 (p) REVERT: E 167 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6008 (ttm110) REVERT: R 101 ASP cc_start: 0.5529 (m-30) cc_final: 0.5298 (t0) REVERT: R 187 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6133 (tpt) REVERT: R 257 GLN cc_start: 0.7133 (mt0) cc_final: 0.6913 (mt0) REVERT: R 287 ASP cc_start: 0.6262 (t0) cc_final: 0.5960 (t0) REVERT: R 288 ASN cc_start: 0.6582 (m-40) cc_final: 0.6094 (m-40) REVERT: R 367 MET cc_start: 0.3669 (OUTLIER) cc_final: 0.3385 (ttt) REVERT: R 382 PHE cc_start: 0.6928 (m-80) cc_final: 0.6587 (m-80) REVERT: R 405 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6197 (mp10) REVERT: A 28 LYS cc_start: 0.6475 (pptt) cc_final: 0.5754 (ptpt) REVERT: A 31 GLN cc_start: 0.6108 (mm110) cc_final: 0.5904 (mm110) REVERT: A 35 GLN cc_start: 0.6277 (tt0) cc_final: 0.5402 (mp-120) REVERT: A 356 ARG cc_start: 0.6962 (ptt-90) cc_final: 0.6628 (ptt-90) REVERT: A 389 ARG cc_start: 0.7500 (ttt90) cc_final: 0.6295 (ttm110) REVERT: A 390 GLN cc_start: 0.6370 (mt0) cc_final: 0.5731 (mp10) REVERT: B 4 LEU cc_start: 0.4104 (OUTLIER) cc_final: 0.3884 (tp) REVERT: B 13 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6572 (tm-30) REVERT: B 195 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7083 (p0) REVERT: B 215 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7300 (mp0) REVERT: B 217 MET cc_start: 0.7240 (ptt) cc_final: 0.6589 (pmm) REVERT: N 5 GLN cc_start: 0.7177 (tt0) cc_final: 0.6360 (tm-30) REVERT: N 25 SER cc_start: 0.6474 (OUTLIER) cc_final: 0.5903 (t) REVERT: N 43 LYS cc_start: 0.6525 (mtpt) cc_final: 0.6240 (mttt) REVERT: N 108 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7015 (m-80) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 0.5498 time to fit residues: 94.6491 Evaluate side-chains 161 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.213710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151945 restraints weight = 24371.583| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.58 r_work: 0.3689 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10470 Z= 0.128 Angle : 0.533 10.113 14195 Z= 0.275 Chirality : 0.042 0.299 1572 Planarity : 0.004 0.059 1785 Dihedral : 5.528 52.459 1520 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.14 % Allowed : 18.57 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1252 helix: 2.11 (0.23), residues: 515 sheet: -0.31 (0.32), residues: 251 loop : -0.44 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.020 0.001 TYR N 60 PHE 0.016 0.001 PHE R 99 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10457) covalent geometry : angle 0.52571 / 0.27 (14168) SS BOND : bond 0.00243 / 0.16 ( 9) SS BOND : angle 0.88179 / 0.45 ( 18) hydrogen bonds : bond 0.03858 / 2.61 ( 518) hydrogen bonds : angle 4.40036 / 3.23 ( 1486) Misc. bond : bond 0.00011 / 0.01 ( 1) link_NAG-ASN : bond 0.00852 / 0.41 ( 3) link_NAG-ASN : angle 3.34662 / 1.96 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6399 (p) REVERT: E 167 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5975 (ttm110) REVERT: R 101 ASP cc_start: 0.5558 (m-30) cc_final: 0.5295 (t0) REVERT: R 187 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6203 (tpt) REVERT: R 257 GLN cc_start: 0.7121 (mt0) cc_final: 0.6871 (mt0) REVERT: R 258 ARG cc_start: 0.7164 (mtm110) cc_final: 0.6640 (mtm110) REVERT: R 287 ASP cc_start: 0.6246 (t0) cc_final: 0.5953 (t0) REVERT: R 288 ASN cc_start: 0.6563 (m-40) cc_final: 0.6074 (m-40) REVERT: R 367 MET cc_start: 0.3670 (OUTLIER) cc_final: 0.3390 (ttt) REVERT: R 382 PHE cc_start: 0.6955 (m-80) cc_final: 0.6564 (m-80) REVERT: R 405 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: A 28 LYS cc_start: 0.6505 (pptt) cc_final: 0.5772 (ptpt) REVERT: A 35 GLN cc_start: 0.6290 (tt0) cc_final: 0.5373 (mp-120) REVERT: A 389 ARG cc_start: 0.7563 (ttt90) cc_final: 0.6278 (ttm110) REVERT: A 390 GLN cc_start: 0.6399 (mt0) cc_final: 0.5706 (mp10) REVERT: B 4 LEU cc_start: 0.4106 (OUTLIER) cc_final: 0.3884 (tp) REVERT: B 13 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6536 (tm-30) REVERT: B 59 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 195 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7067 (p0) REVERT: B 215 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7317 (mp0) REVERT: B 217 MET cc_start: 0.7267 (ptt) cc_final: 0.6629 (pmm) REVERT: N 5 GLN cc_start: 0.7220 (tt0) cc_final: 0.6610 (mt0) REVERT: N 25 SER cc_start: 0.6512 (OUTLIER) cc_final: 0.5955 (t) REVERT: N 43 LYS cc_start: 0.6527 (mtpt) cc_final: 0.6247 (mttt) REVERT: N 108 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7094 (m-80) outliers start: 33 outliers final: 20 residues processed: 154 average time/residue: 0.5191 time to fit residues: 85.9311 Evaluate side-chains 158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 346 MET Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 0.0030 chunk 38 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 10 GLN B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.215295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155465 restraints weight = 17135.006| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.08 r_work: 0.3735 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10470 Z= 0.109 Angle : 0.521 9.720 14195 Z= 0.270 Chirality : 0.042 0.299 1572 Planarity : 0.003 0.059 1785 Dihedral : 5.412 54.150 1520 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.95 % Allowed : 18.95 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1252 helix: 2.17 (0.23), residues: 515 sheet: -0.25 (0.32), residues: 250 loop : -0.41 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 45 TYR 0.019 0.001 TYR N 60 PHE 0.013 0.001 PHE A 212 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (10457) covalent geometry : angle 0.51359 / 0.27 (14168) SS BOND : bond 0.00232 / 0.15 ( 9) SS BOND : angle 0.77061 / 0.41 ( 18) hydrogen bonds : bond 0.03636 / 2.46 ( 518) hydrogen bonds : angle 4.32283 / 3.17 ( 1486) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00858 / 0.41 ( 3) link_NAG-ASN : angle 3.31187 / 1.94 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.92 seconds wall clock time: 83 minutes 45.38 seconds (5025.38 seconds total)