Starting phenix.real_space_refine on Thu Jul 2 20:05:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyy_26199/07_2026/7tyy_26199.cif" } resolution = 3.0 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= -0.000 sd= 0.004 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 68 5.16 5 C 6265 2.51 5 N 1676 2.21 5 O 1793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 9802 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 568 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 7, 'GLN:plan1': 3, 'PHE:plan': 4, 'ASP:plan': 8, 'TRP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 150 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} 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: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2941 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1895 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {'NAG': 1, 'PLM': 5, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.84, per 1000 atoms: 0.19 Number of scatterers: 9802 At special positions: 0 Unit cell: (82.82, 99.22, 156.62, 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 68 16.00 O 1793 8.00 N 1676 7.00 C 6265 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 1 " - pdb=" SG CYS P 7 " distance=2.02 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=2.03 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 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 254.1 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 44.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 5.238A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 107 removed outlier: 3.805A pdb=" N SER E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.678A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 149 removed outlier: 3.944A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 165 removed outlier: 3.765A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.522A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 21 Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.707A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.332A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.544A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.552A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.581A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 249 removed outlier: 3.794A 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 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.519A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (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 329 Proline residue: R 304 - end of helix removed outlier: 3.555A pdb=" N ASN R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG R 321 " --> pdb=" O LEU R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 removed outlier: 3.803A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 381 removed outlier: 3.556A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) 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: 3.687A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.660A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 58' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.550A 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 293 through 303 removed outlier: 3.869A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.116A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.527A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 4.389A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.558A 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 10 through 24 removed outlier: 4.156A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.865A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.532A pdb=" N SER R 91 " --> pdb=" O LYS R 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.777A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.962A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.949A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.513A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.436A 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: 6.520A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.734A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.230A 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: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.155A 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: 3.701A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.472A 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: 6.106A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1320 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: 1.31 Time building geometry restraints manager: 0.87 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: 1597 1.32 - 1.44: 2765 1.44 - 1.57: 5558 1.57 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 10014 Sorted by residual: bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N HIS R 302 " pdb=" CA HIS R 302 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.23e+00 bond pdb=" N ILE R 301 " pdb=" CA ILE R 301 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.23e-02 6.61e+03 7.38e+00 bond pdb=" N VAL R 305 " pdb=" CA VAL R 305 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.09e+00 bond pdb=" N THR P 27 " pdb=" CA THR P 27 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.08e-02 8.57e+03 6.68e+00 ... (remaining 10009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 13558 3.84 - 7.68: 24 7.68 - 11.51: 0 11.51 - 15.35: 0 15.35 - 19.19: 2 Bond angle restraints: 13584 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 95.31 16.69 1.40e+00 5.10e-01 1.42e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 144.19 -19.19 4.10e+00 5.95e-02 2.19e+01 angle pdb=" N LEU R 298 " pdb=" CA LEU R 298 " pdb=" C LEU R 298 " ideal model delta sigma weight residual 113.18 107.94 5.24 1.21e+00 6.83e-01 1.88e+01 angle pdb=" O THR P 31 " pdb=" C THR P 31 " pdb=" N PRO P 32 " ideal model delta sigma weight residual 121.66 125.45 -3.79 9.40e-01 1.13e+00 1.62e+01 angle pdb=" N THR P 27 " pdb=" CA THR P 27 " pdb=" C THR P 27 " ideal model delta sigma weight residual 112.30 107.07 5.23 1.36e+00 5.41e-01 1.48e+01 ... (remaining 13579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5453 17.72 - 35.44: 352 35.44 - 53.16: 93 53.16 - 70.88: 15 70.88 - 88.60: 12 Dihedral angle restraints: 5925 sinusoidal: 2276 harmonic: 3649 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 93.00 173.02 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -128.76 42.76 1 1.00e+01 1.00e-02 2.55e+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 -47.08 -38.92 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 5922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1174 0.043 - 0.087: 259 0.087 - 0.130: 75 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CB VAL P 8 " pdb=" CA VAL P 8 " pdb=" CG1 VAL P 8 " pdb=" CG2 VAL P 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ALA R 307 " pdb=" N ALA R 307 " pdb=" C ALA R 307 " pdb=" CB ALA R 307 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1515 not shown) Planarity restraints: 1725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN P 26 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASN P 26 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN P 26 " 0.017 2.00e-02 2.50e+03 pdb=" N THR P 27 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 299 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C TYR R 299 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR R 299 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE R 300 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.033 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO P 32 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.026 5.00e-02 4.00e+02 ... (remaining 1722 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 330 2.72 - 3.26: 9996 3.26 - 3.81: 16541 3.81 - 4.35: 22015 4.35 - 4.90: 35463 Nonbonded interactions: 84345 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.174 3.040 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.265 3.120 ... (remaining 84340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.460 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.003 0.108 10025 Z= 0.222 Angle : 0.576 19.189 13605 Z= 0.350 Chirality : 0.041 0.217 1518 Planarity : 0.003 0.045 1724 Dihedral : 13.321 88.597 3538 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.03 % Allowed : 14.04 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -3.39 (0.20), residues: 1230 helix: -2.79 (0.17), residues: 473 sheet: -2.22 (0.30), residues: 215 loop : -1.51 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.009 0.001 TYR N 60 PHE 0.008 0.001 PHE E 128 TRP 0.009 0.001 TRP R 76 HIS 0.003 0.000 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (10014) covalent geometry : angle 0.57466 / 0.35 (13584) SS BOND : bond 0.00462 / 0.24 ( 9) SS BOND : angle 1.04397 / 0.66 ( 18) hydrogen bonds : bond 0.26749 / 18.57 ( 468) hydrogen bonds : angle 9.63821 / 6.91 ( 1320) Misc. bond : bond 0.10769 / 5.67 ( 1) link_NAG-ASN : bond 0.00192 / 0.10 ( 1) link_NAG-ASN : angle 1.32165 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: E 103 PHE cc_start: 0.6332 (m-10) cc_final: 0.5853 (m-80) REVERT: R 48 MET cc_start: 0.6999 (ttm) cc_final: 0.6506 (ttt) REVERT: R 49 MET cc_start: 0.7668 (mmm) cc_final: 0.6925 (mpp) REVERT: R 99 PHE cc_start: 0.7522 (m-80) cc_final: 0.7302 (m-80) REVERT: R 143 LYS cc_start: 0.7028 (tttt) cc_final: 0.6358 (mtmt) REVERT: R 213 ARG cc_start: 0.5391 (mtt90) cc_final: 0.4915 (mtp-110) REVERT: R 230 MET cc_start: 0.7091 (mtm) cc_final: 0.6766 (ttp) REVERT: R 346 MET cc_start: 0.6678 (mmp) cc_final: 0.6056 (ptp) REVERT: A 221 MET cc_start: 0.7775 (ttm) cc_final: 0.7419 (ttp) REVERT: A 265 ARG cc_start: 0.6230 (mmt180) cc_final: 0.5879 (mtt90) REVERT: B 19 ARG cc_start: 0.6639 (mtm180) cc_final: 0.6248 (mtm180) REVERT: G 17 GLU cc_start: 0.6130 (mm-30) cc_final: 0.5789 (pt0) REVERT: G 21 MET cc_start: 0.6199 (mmm) cc_final: 0.5977 (ttt) REVERT: N 106 ASP cc_start: 0.6811 (p0) cc_final: 0.6401 (p0) outliers start: 20 outliers final: 9 residues processed: 239 average time/residue: 0.5205 time to fit residues: 133.2210 Evaluate side-chains 169 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 186 ASN R 286 ASN R 399 GLN A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 236 GLN A 264 ASN A 278 ASN A 294 GLN A 371 ASN B 175 GLN B 266 HIS B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.179039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143829 restraints weight = 11147.906| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.39 r_work: 0.3445 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10025 Z= 0.187 Angle : 0.584 7.350 13605 Z= 0.309 Chirality : 0.043 0.182 1518 Planarity : 0.004 0.043 1724 Dihedral : 5.961 39.128 1459 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.76 % Allowed : 17.70 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.62 (0.23), residues: 1230 helix: -0.69 (0.22), residues: 487 sheet: -1.61 (0.31), residues: 218 loop : -1.01 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 380 TYR 0.023 0.002 TYR A 358 PHE 0.020 0.002 PHE R 359 TRP 0.020 0.002 TRP B 169 HIS 0.008 0.001 HIS R 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (10014) covalent geometry : angle 0.58024 / 0.31 (13584) SS BOND : bond 0.00447 / 0.25 ( 9) SS BOND : angle 1.78567 / 1.19 ( 18) hydrogen bonds : bond 0.04727 / 3.35 ( 468) hydrogen bonds : angle 5.85156 / 4.20 ( 1320) Misc. bond : bond 0.00090 / 0.05 ( 1) link_NAG-ASN : bond 0.00165 / 0.09 ( 1) link_NAG-ASN : angle 1.04481 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.472 Fit side-chains REVERT: E 103 PHE cc_start: 0.6701 (m-10) cc_final: 0.6212 (m-80) REVERT: R 49 MET cc_start: 0.7824 (mmm) cc_final: 0.6799 (mpp) REVERT: R 52 GLN cc_start: 0.7537 (tt0) cc_final: 0.7160 (tm-30) REVERT: R 137 PHE cc_start: 0.7400 (m-80) cc_final: 0.7041 (m-80) REVERT: R 143 LYS cc_start: 0.7003 (tttt) cc_final: 0.6247 (mtmt) REVERT: R 230 MET cc_start: 0.7487 (mtm) cc_final: 0.7073 (ttp) REVERT: R 240 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7347 (mm-30) REVERT: R 259 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6913 (mp) REVERT: R 306 MET cc_start: 0.8388 (mmm) cc_final: 0.8030 (mmt) REVERT: A 31 GLN cc_start: 0.7704 (tp40) cc_final: 0.6999 (tt0) REVERT: A 221 MET cc_start: 0.8396 (ttm) cc_final: 0.8069 (ttp) REVERT: A 299 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6068 (tt0) REVERT: B 130 GLU cc_start: 0.5165 (OUTLIER) cc_final: 0.4662 (mp0) REVERT: B 217 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6988 (ppp) REVERT: N 5 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6350 (mm-40) REVERT: N 87 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8204 (mttt) outliers start: 37 outliers final: 16 residues processed: 177 average time/residue: 0.5073 time to fit residues: 97.4053 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 92 TYR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 113 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 336 HIS A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.180499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145885 restraints weight = 11182.348| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.38 r_work: 0.3544 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10025 Z= 0.120 Angle : 0.511 6.614 13605 Z= 0.268 Chirality : 0.041 0.149 1518 Planarity : 0.003 0.033 1724 Dihedral : 5.376 40.548 1451 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.46 % Allowed : 18.51 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.92 (0.23), residues: 1230 helix: 0.12 (0.24), residues: 488 sheet: -1.38 (0.32), residues: 221 loop : -0.81 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 67 TYR 0.012 0.001 TYR A 358 PHE 0.007 0.001 PHE A 212 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS R 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10014) covalent geometry : angle 0.50868 / 0.27 (13584) SS BOND : bond 0.00419 / 0.22 ( 9) SS BOND : angle 1.30963 / 0.87 ( 18) hydrogen bonds : bond 0.03866 / 2.77 ( 468) hydrogen bonds : angle 5.24464 / 3.77 ( 1320) Misc. bond : bond 0.00018 / 0.01 ( 1) link_NAG-ASN : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : angle 0.96288 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.268 Fit side-chains REVERT: E 103 PHE cc_start: 0.6571 (m-10) cc_final: 0.6094 (m-80) REVERT: R 49 MET cc_start: 0.7906 (mmm) cc_final: 0.6402 (mpp) REVERT: R 52 GLN cc_start: 0.7646 (tt0) cc_final: 0.7215 (tm-30) REVERT: R 143 LYS cc_start: 0.7050 (tttt) cc_final: 0.6376 (mtmt) REVERT: R 230 MET cc_start: 0.7449 (mtm) cc_final: 0.7190 (ttp) REVERT: R 240 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7500 (mm-30) REVERT: R 321 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6776 (ttm170) REVERT: A 31 GLN cc_start: 0.7680 (tp40) cc_final: 0.6995 (tt0) REVERT: A 221 MET cc_start: 0.8279 (ttm) cc_final: 0.7917 (ttp) REVERT: A 299 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: B 217 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7167 (ppp) REVERT: G 38 MET cc_start: 0.7948 (ttp) cc_final: 0.7739 (ttm) REVERT: N 5 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6372 (mm-40) REVERT: N 87 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8391 (mttt) REVERT: N 106 ASP cc_start: 0.7321 (p0) cc_final: 0.7088 (p0) outliers start: 34 outliers final: 14 residues processed: 176 average time/residue: 0.4425 time to fit residues: 84.2708 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 92 TYR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 41 HIS A 236 GLN A 357 HIS B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139751 restraints weight = 11529.203| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.74 r_work: 0.3473 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10025 Z= 0.130 Angle : 0.517 8.460 13605 Z= 0.270 Chirality : 0.041 0.197 1518 Planarity : 0.003 0.039 1724 Dihedral : 5.331 42.023 1450 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.46 % Allowed : 19.43 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.52 (0.24), residues: 1230 helix: 0.54 (0.24), residues: 497 sheet: -1.17 (0.33), residues: 220 loop : -0.71 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 67 TYR 0.017 0.001 TYR R 372 PHE 0.019 0.001 PHE R 119 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10014) covalent geometry : angle 0.51525 / 0.27 (13584) SS BOND : bond 0.00395 / 0.21 ( 9) SS BOND : angle 1.23055 / 0.84 ( 18) hydrogen bonds : bond 0.03616 / 2.59 ( 468) hydrogen bonds : angle 4.97173 / 3.59 ( 1320) Misc. bond : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 1.01667 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.376 Fit side-chains REVERT: E 103 PHE cc_start: 0.6534 (m-80) cc_final: 0.6018 (m-80) REVERT: R 49 MET cc_start: 0.7876 (mmm) cc_final: 0.6326 (mpp) REVERT: R 52 GLN cc_start: 0.7668 (tt0) cc_final: 0.7068 (tm-30) REVERT: R 77 ASP cc_start: 0.7823 (p0) cc_final: 0.7595 (p0) REVERT: R 110 LYS cc_start: 0.4263 (tttp) cc_final: 0.3930 (ttmm) REVERT: R 143 LYS cc_start: 0.7053 (tttt) cc_final: 0.6320 (mtmt) REVERT: R 240 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7499 (mm-30) REVERT: R 259 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6974 (mp) REVERT: R 321 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6726 (ttm170) REVERT: R 405 GLN cc_start: 0.6207 (mp10) cc_final: 0.6000 (mp10) REVERT: A 31 GLN cc_start: 0.7636 (tp40) cc_final: 0.6960 (tt0) REVERT: A 35 GLN cc_start: 0.7385 (mp10) cc_final: 0.7160 (mm-40) REVERT: A 221 MET cc_start: 0.8235 (ttm) cc_final: 0.7855 (ttp) REVERT: B 130 GLU cc_start: 0.5169 (OUTLIER) cc_final: 0.4807 (mp0) REVERT: B 217 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7178 (ppp) REVERT: G 38 MET cc_start: 0.7869 (ttp) cc_final: 0.7651 (ttm) REVERT: N 1 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: N 87 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8427 (mttm) outliers start: 34 outliers final: 16 residues processed: 165 average time/residue: 0.4799 time to fit residues: 85.5547 Evaluate side-chains 157 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 357 HIS N 31 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138475 restraints weight = 11414.530| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.69 r_work: 0.3467 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10025 Z= 0.136 Angle : 0.515 7.778 13605 Z= 0.269 Chirality : 0.041 0.165 1518 Planarity : 0.003 0.042 1724 Dihedral : 5.396 44.581 1450 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.87 % Allowed : 20.24 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.37 (0.24), residues: 1230 helix: 0.68 (0.24), residues: 501 sheet: -1.17 (0.33), residues: 226 loop : -0.60 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 67 TYR 0.014 0.001 TYR A 358 PHE 0.013 0.001 PHE R 119 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (10014) covalent geometry : angle 0.51260 / 0.27 (13584) SS BOND : bond 0.00410 / 0.22 ( 9) SS BOND : angle 1.39246 / 1.01 ( 18) hydrogen bonds : bond 0.03520 / 2.53 ( 468) hydrogen bonds : angle 4.81463 / 3.48 ( 1320) Misc. bond : bond 0.00031 / 0.02 ( 1) link_NAG-ASN : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : angle 1.02182 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.376 Fit side-chains REVERT: E 103 PHE cc_start: 0.6478 (m-80) cc_final: 0.5980 (m-80) REVERT: R 49 MET cc_start: 0.7827 (mmm) cc_final: 0.6313 (mpp) REVERT: R 52 GLN cc_start: 0.7692 (tt0) cc_final: 0.7065 (tm-30) REVERT: R 77 ASP cc_start: 0.7809 (p0) cc_final: 0.7515 (p0) REVERT: R 110 LYS cc_start: 0.4322 (tttp) cc_final: 0.3990 (ttmm) REVERT: R 143 LYS cc_start: 0.7059 (tttt) cc_final: 0.6322 (mtmt) REVERT: R 240 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7486 (mm-30) REVERT: R 321 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6747 (ttm170) REVERT: R 405 GLN cc_start: 0.6311 (mp10) cc_final: 0.6069 (mp10) REVERT: A 31 GLN cc_start: 0.7576 (tp40) cc_final: 0.6920 (tt0) REVERT: A 221 MET cc_start: 0.8230 (ttm) cc_final: 0.7889 (ttp) REVERT: A 299 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6220 (tt0) REVERT: B 130 GLU cc_start: 0.5172 (OUTLIER) cc_final: 0.4758 (mp0) REVERT: B 217 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7261 (ppp) REVERT: G 38 MET cc_start: 0.7845 (ttp) cc_final: 0.7622 (ttm) REVERT: N 1 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7183 (tt0) outliers start: 38 outliers final: 19 residues processed: 173 average time/residue: 0.4591 time to fit residues: 86.4538 Evaluate side-chains 161 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 41 HIS A 279 ASN A 357 HIS N 31 ASN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137759 restraints weight = 11543.528| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.80 r_work: 0.3461 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10025 Z= 0.133 Angle : 0.510 7.050 13605 Z= 0.267 Chirality : 0.041 0.207 1518 Planarity : 0.003 0.046 1724 Dihedral : 5.394 46.551 1450 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.17 % Allowed : 20.96 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.24 (0.24), residues: 1230 helix: 0.81 (0.24), residues: 503 sheet: -1.15 (0.33), residues: 233 loop : -0.52 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 67 TYR 0.019 0.001 TYR R 372 PHE 0.009 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 0.00299 / 0.13 (10014) covalent geometry : angle 0.50814 / 0.27 (13584) SS BOND : bond 0.00419 / 0.24 ( 9) SS BOND : angle 1.16148 / 0.80 ( 18) hydrogen bonds : bond 0.03458 / 2.49 ( 468) hydrogen bonds : angle 4.75283 / 3.44 ( 1320) Misc. bond : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : bond 0.00055 / 0.03 ( 1) link_NAG-ASN : angle 0.98581 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.290 Fit side-chains REVERT: E 103 PHE cc_start: 0.6458 (m-80) cc_final: 0.5957 (m-80) REVERT: R 49 MET cc_start: 0.7817 (mmm) cc_final: 0.6316 (mpp) REVERT: R 52 GLN cc_start: 0.7694 (tt0) cc_final: 0.7095 (tt0) REVERT: R 77 ASP cc_start: 0.7830 (p0) cc_final: 0.7540 (p0) REVERT: R 110 LYS cc_start: 0.4317 (tttp) cc_final: 0.3976 (ttmm) REVERT: R 143 LYS cc_start: 0.7028 (tttt) cc_final: 0.6309 (mtmt) REVERT: R 240 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7470 (mm-30) REVERT: R 321 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6757 (ttm170) REVERT: R 405 GLN cc_start: 0.6440 (mp10) cc_final: 0.6176 (mp10) REVERT: A 12 GLN cc_start: 0.4790 (OUTLIER) cc_final: 0.3389 (tm130) REVERT: A 35 GLN cc_start: 0.7368 (mp10) cc_final: 0.7103 (tp40) REVERT: A 221 MET cc_start: 0.8231 (ttm) cc_final: 0.7859 (ttp) REVERT: A 299 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6293 (tt0) REVERT: A 334 VAL cc_start: 0.7787 (t) cc_final: 0.7514 (p) REVERT: B 130 GLU cc_start: 0.5239 (OUTLIER) cc_final: 0.4814 (mp0) REVERT: B 217 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7316 (ppp) REVERT: G 38 MET cc_start: 0.7854 (ttp) cc_final: 0.7627 (ttm) REVERT: N 1 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7063 (tt0) outliers start: 41 outliers final: 21 residues processed: 165 average time/residue: 0.4470 time to fit residues: 80.1001 Evaluate side-chains 164 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 279 ASN A 357 HIS N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.162787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127493 restraints weight = 11558.603| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.72 r_work: 0.3340 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 10025 Z= 0.405 Angle : 0.768 8.945 13605 Z= 0.401 Chirality : 0.051 0.246 1518 Planarity : 0.006 0.049 1724 Dihedral : 7.701 54.923 1450 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.48 % Allowed : 20.75 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.90 (0.23), residues: 1230 helix: 0.05 (0.23), residues: 492 sheet: -1.34 (0.32), residues: 230 loop : -0.68 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 67 TYR 0.026 0.003 TYR R 374 PHE 0.018 0.003 PHE A 315 TRP 0.023 0.003 TRP B 297 HIS 0.008 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00921 / 0.40 (10014) covalent geometry : angle 0.76535 / 0.40 (13584) SS BOND : bond 0.00803 / 0.43 ( 9) SS BOND : angle 1.88085 / 1.32 ( 18) hydrogen bonds : bond 0.04696 / 3.35 ( 468) hydrogen bonds : angle 5.68886 / 4.15 ( 1320) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00507 / 0.27 ( 1) link_NAG-ASN : angle 1.61355 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.380 Fit side-chains REVERT: E 103 PHE cc_start: 0.6421 (m-80) cc_final: 0.6019 (m-80) REVERT: R 49 MET cc_start: 0.7696 (mmm) cc_final: 0.6801 (mpp) REVERT: R 52 GLN cc_start: 0.7751 (tt0) cc_final: 0.7500 (tt0) REVERT: R 77 ASP cc_start: 0.7853 (p0) cc_final: 0.7533 (p0) REVERT: R 143 LYS cc_start: 0.7024 (tttt) cc_final: 0.6316 (mtmt) REVERT: R 321 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7217 (ttm170) REVERT: A 12 GLN cc_start: 0.4280 (OUTLIER) cc_final: 0.3545 (mm-40) REVERT: A 221 MET cc_start: 0.8317 (ttm) cc_final: 0.7965 (ttp) REVERT: A 299 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6268 (tt0) REVERT: B 59 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7283 (t80) REVERT: B 130 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4856 (mp0) REVERT: G 38 MET cc_start: 0.7892 (ttp) cc_final: 0.7649 (ttm) REVERT: N 1 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6779 (tp40) outliers start: 44 outliers final: 23 residues processed: 166 average time/residue: 0.4544 time to fit residues: 82.0216 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132996 restraints weight = 11401.524| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.50 r_work: 0.3437 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10025 Z= 0.142 Angle : 0.550 8.126 13605 Z= 0.288 Chirality : 0.042 0.183 1518 Planarity : 0.004 0.048 1724 Dihedral : 6.587 54.624 1450 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.95 % Allowed : 22.99 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.47 (0.24), residues: 1230 helix: 0.64 (0.23), residues: 491 sheet: -1.18 (0.33), residues: 224 loop : -0.71 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 67 TYR 0.022 0.001 TYR R 284 PHE 0.011 0.001 PHE A 222 TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10014) covalent geometry : angle 0.54783 / 0.29 (13584) SS BOND : bond 0.00250 / 0.16 ( 9) SS BOND : angle 1.46642 / 1.04 ( 18) hydrogen bonds : bond 0.03631 / 2.62 ( 468) hydrogen bonds : angle 4.99369 / 3.64 ( 1320) Misc. bond : bond 0.00027 / 0.01 ( 1) link_NAG-ASN : bond 0.00011 / 0.01 ( 1) link_NAG-ASN : angle 1.11408 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.360 Fit side-chains REVERT: E 103 PHE cc_start: 0.6297 (m-80) cc_final: 0.5822 (m-80) REVERT: R 49 MET cc_start: 0.7715 (mmm) cc_final: 0.6328 (mpp) REVERT: R 52 GLN cc_start: 0.7660 (tt0) cc_final: 0.7425 (tt0) REVERT: R 77 ASP cc_start: 0.7919 (p0) cc_final: 0.7667 (p0) REVERT: R 143 LYS cc_start: 0.6955 (tttt) cc_final: 0.6185 (mtmt) REVERT: R 321 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6833 (ttm170) REVERT: R 346 MET cc_start: 0.7490 (mmp) cc_final: 0.6318 (ttp) REVERT: A 221 MET cc_start: 0.8294 (ttm) cc_final: 0.7892 (ttp) REVERT: A 299 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6268 (tt0) REVERT: A 334 VAL cc_start: 0.7826 (t) cc_final: 0.7553 (p) REVERT: B 217 MET cc_start: 0.8053 (mmm) cc_final: 0.7798 (mmm) REVERT: G 38 MET cc_start: 0.7852 (ttp) cc_final: 0.7591 (ttm) REVERT: N 1 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6954 (tt0) outliers start: 29 outliers final: 16 residues processed: 163 average time/residue: 0.4476 time to fit residues: 79.2513 Evaluate side-chains 146 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.168769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132455 restraints weight = 11392.845| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.49 r_work: 0.3435 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10025 Z= 0.157 Angle : 0.560 9.951 13605 Z= 0.292 Chirality : 0.043 0.279 1518 Planarity : 0.004 0.050 1724 Dihedral : 6.482 55.468 1450 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.15 % Allowed : 23.19 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.30 (0.24), residues: 1230 helix: 0.80 (0.24), residues: 492 sheet: -1.19 (0.32), residues: 235 loop : -0.56 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 67 TYR 0.019 0.001 TYR R 284 PHE 0.019 0.001 PHE A 222 TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (10014) covalent geometry : angle 0.55632 / 0.29 (13584) SS BOND : bond 0.00207 / 0.13 ( 9) SS BOND : angle 1.85833 / 1.29 ( 18) hydrogen bonds : bond 0.03625 / 2.61 ( 468) hydrogen bonds : angle 4.92304 / 3.60 ( 1320) Misc. bond : bond 0.00018 / 0.01 ( 1) link_NAG-ASN : bond 0.00026 / 0.01 ( 1) link_NAG-ASN : angle 1.11058 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.268 Fit side-chains REVERT: E 103 PHE cc_start: 0.6283 (m-80) cc_final: 0.5810 (m-80) REVERT: R 49 MET cc_start: 0.7752 (mmm) cc_final: 0.6277 (mpp) REVERT: R 52 GLN cc_start: 0.7621 (tt0) cc_final: 0.6928 (tm-30) REVERT: R 77 ASP cc_start: 0.7880 (p0) cc_final: 0.7608 (p0) REVERT: R 143 LYS cc_start: 0.6957 (tttt) cc_final: 0.6228 (mtmt) REVERT: R 321 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6855 (ttm170) REVERT: A 31 GLN cc_start: 0.7615 (tp-100) cc_final: 0.6824 (tt0) REVERT: A 221 MET cc_start: 0.8310 (ttm) cc_final: 0.7896 (ttp) REVERT: A 299 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: B 217 MET cc_start: 0.8065 (mmm) cc_final: 0.7818 (mmm) REVERT: G 38 MET cc_start: 0.7847 (ttp) cc_final: 0.7609 (ttm) REVERT: N 1 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6759 (tp40) outliers start: 31 outliers final: 18 residues processed: 151 average time/residue: 0.4718 time to fit residues: 77.3252 Evaluate side-chains 147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 6 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 279 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137525 restraints weight = 11392.882| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.70 r_work: 0.3455 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10025 Z= 0.129 Angle : 0.546 9.548 13605 Z= 0.284 Chirality : 0.041 0.205 1518 Planarity : 0.004 0.052 1724 Dihedral : 6.145 56.623 1450 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.34 % Allowed : 24.11 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.08 (0.24), residues: 1230 helix: 0.97 (0.24), residues: 495 sheet: -1.13 (0.33), residues: 239 loop : -0.40 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 67 TYR 0.016 0.001 TYR R 372 PHE 0.014 0.001 PHE A 222 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10014) covalent geometry : angle 0.53607 / 0.28 (13584) SS BOND : bond 0.00536 / 0.43 ( 9) SS BOND : angle 2.82962 / 2.26 ( 18) hydrogen bonds : bond 0.03408 / 2.46 ( 468) hydrogen bonds : angle 4.71885 / 3.45 ( 1320) Misc. bond : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 0.99432 / 0.52 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.266 Fit side-chains REVERT: E 103 PHE cc_start: 0.6245 (m-80) cc_final: 0.5788 (m-80) REVERT: R 49 MET cc_start: 0.7835 (mmm) cc_final: 0.6444 (mpp) REVERT: R 52 GLN cc_start: 0.7646 (tt0) cc_final: 0.7001 (tm-30) REVERT: R 77 ASP cc_start: 0.7886 (p0) cc_final: 0.7617 (p0) REVERT: R 143 LYS cc_start: 0.6967 (tttt) cc_final: 0.6283 (mtmt) REVERT: R 321 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6860 (ttm170) REVERT: R 346 MET cc_start: 0.7472 (mmp) cc_final: 0.6397 (ptp) REVERT: A 221 MET cc_start: 0.8246 (ttm) cc_final: 0.7861 (ttp) REVERT: A 299 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: A 334 VAL cc_start: 0.7752 (t) cc_final: 0.7478 (p) REVERT: B 217 MET cc_start: 0.8081 (mmm) cc_final: 0.7849 (mmm) REVERT: N 1 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6819 (tp40) outliers start: 23 outliers final: 16 residues processed: 156 average time/residue: 0.4423 time to fit residues: 75.0565 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 279 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134876 restraints weight = 11461.515| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.90 r_work: 0.3415 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10025 Z= 0.180 Angle : 0.588 9.762 13605 Z= 0.303 Chirality : 0.043 0.235 1518 Planarity : 0.004 0.050 1724 Dihedral : 6.499 59.108 1450 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.14 % Allowed : 24.92 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.20 (0.24), residues: 1230 helix: 0.87 (0.23), residues: 500 sheet: -1.30 (0.32), residues: 233 loop : -0.41 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 67 TYR 0.018 0.002 TYR A 358 PHE 0.021 0.002 PHE R 119 TRP 0.015 0.002 TRP R 236 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (10014) covalent geometry : angle 0.58061 / 0.30 (13584) SS BOND : bond 0.00226 / 0.14 ( 9) SS BOND : angle 2.60800 / 2.06 ( 18) hydrogen bonds : bond 0.03624 / 2.61 ( 468) hydrogen bonds : angle 4.85237 / 3.56 ( 1320) Misc. bond : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : angle 1.19437 / 0.63 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.69 seconds wall clock time: 56 minutes 48.41 seconds (3408.41 seconds total)