Starting phenix.real_space_refine on Wed Mar 4 02:10:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyy_26199/03_2026/7tyy_26199.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyy_26199/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tyy_26199/03_2026/7tyy_26199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyy_26199/03_2026/7tyy_26199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyy_26199/03_2026/7tyy_26199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyy_26199/03_2026/7tyy_26199.map" } 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-5986/lib/python3.9/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 dihedrals: 3 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: 2.34, per 1000 atoms: 0.24 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: 0.64 Conformation dependent library (CDL) restraints added in 394.1 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: 0.27 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: 1.64 Time building geometry restraints manager: 0.85 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: 5576 17.72 - 35.44: 356 35.44 - 53.16: 98 53.16 - 70.88: 20 70.88 - 88.60: 12 Dihedral angle restraints: 6062 sinusoidal: 2413 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 6059 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.040 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 13.400 88.597 3675 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 covalent geometry : bond 0.00319 (10014) covalent geometry : angle 0.57466 (13584) SS BOND : bond 0.00462 ( 9) SS BOND : angle 1.04397 ( 18) hydrogen bonds : bond 0.26749 ( 468) hydrogen bonds : angle 9.63821 ( 1320) Misc. bond : bond 0.10769 ( 1) link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 1.32165 ( 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 : 0.382 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: 0.6052 time to fit residues: 154.1904 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 : 0.379 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 357 HIS 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143340 restraints weight = 11132.480| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.41 r_work: 0.3437 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2104 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= 0.189 Angle : 0.585 7.541 13605 Z= 0.310 Chirality : 0.043 0.184 1518 Planarity : 0.004 0.042 1724 Dihedral : 7.096 58.515 1596 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.27 % Allowed : 17.40 % Favored : 78.33 % 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: -1.65 (0.22), residues: 1230 helix: -0.72 (0.22), residues: 486 sheet: -1.59 (0.31), residues: 216 loop : -1.05 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 380 TYR 0.023 0.002 TYR A 358 PHE 0.021 0.002 PHE R 359 TRP 0.021 0.002 TRP B 169 HIS 0.009 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00422 (10014) covalent geometry : angle 0.58150 (13584) SS BOND : bond 0.00548 ( 9) SS BOND : angle 1.72918 ( 18) hydrogen bonds : bond 0.04813 ( 468) hydrogen bonds : angle 5.84383 ( 1320) Misc. bond : bond 0.00029 ( 1) link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 1.18580 ( 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 195 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.243 Fit side-chains REVERT: E 103 PHE cc_start: 0.6678 (m-10) cc_final: 0.6184 (m-80) REVERT: R 49 MET cc_start: 0.7768 (mmm) cc_final: 0.6179 (mpp) REVERT: R 52 GLN cc_start: 0.7532 (tt0) cc_final: 0.7116 (tm-30) REVERT: R 137 PHE cc_start: 0.7441 (m-80) cc_final: 0.7090 (m-80) REVERT: R 143 LYS cc_start: 0.6976 (tttt) cc_final: 0.6196 (mtmt) REVERT: R 230 MET cc_start: 0.7459 (mtm) cc_final: 0.7062 (ttp) REVERT: R 306 MET cc_start: 0.8426 (mmm) cc_final: 0.8208 (mmt) REVERT: R 321 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7000 (ttm170) REVERT: A 31 GLN cc_start: 0.7744 (tp40) cc_final: 0.7007 (tt0) REVERT: A 221 MET cc_start: 0.8375 (ttm) cc_final: 0.8030 (ttp) REVERT: A 299 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6060 (tt0) REVERT: B 130 GLU cc_start: 0.5144 (OUTLIER) cc_final: 0.4646 (mp0) REVERT: B 217 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6986 (ppp) REVERT: N 87 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8150 (mttt) outliers start: 42 outliers final: 17 residues processed: 183 average time/residue: 0.4899 time to fit residues: 96.9048 Evaluate side-chains 154 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 321 ARG 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 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 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: 0.3980 chunk 113 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 43 optimal weight: 0.1980 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 268 ASN 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 = 0.4105 r_free = 0.4105 target = 0.181463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149203 restraints weight = 11168.091| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.73 r_work: 0.3465 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10025 Z= 0.110 Angle : 0.505 6.605 13605 Z= 0.265 Chirality : 0.040 0.176 1518 Planarity : 0.003 0.033 1724 Dihedral : 6.579 59.986 1588 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.66 % Allowed : 18.51 % Favored : 77.82 % 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: -0.87 (0.24), residues: 1230 helix: 0.15 (0.23), residues: 497 sheet: -1.40 (0.32), residues: 221 loop : -0.75 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 67 TYR 0.012 0.001 TYR R 284 PHE 0.007 0.001 PHE B 151 TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00240 (10014) covalent geometry : angle 0.50313 (13584) SS BOND : bond 0.00396 ( 9) SS BOND : angle 1.23966 ( 18) hydrogen bonds : bond 0.03737 ( 468) hydrogen bonds : angle 5.11921 ( 1320) Misc. bond : bond 0.00024 ( 1) link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 1.09088 ( 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 193 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.430 Fit side-chains REVERT: E 103 PHE cc_start: 0.6575 (m-10) cc_final: 0.6042 (m-80) REVERT: R 49 MET cc_start: 0.7830 (mmm) cc_final: 0.6308 (mpp) REVERT: R 52 GLN cc_start: 0.7525 (tt0) cc_final: 0.7064 (tm-30) REVERT: R 110 LYS cc_start: 0.4217 (tttp) cc_final: 0.3823 (ttmm) REVERT: R 143 LYS cc_start: 0.7025 (tttt) cc_final: 0.6274 (mtmt) REVERT: R 230 MET cc_start: 0.7448 (mtm) cc_final: 0.7130 (ttp) REVERT: R 240 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7533 (mm-30) REVERT: R 306 MET cc_start: 0.8469 (mmm) cc_final: 0.8259 (mmt) REVERT: R 332 GLU cc_start: 0.6381 (tt0) cc_final: 0.5890 (tt0) REVERT: A 31 GLN cc_start: 0.7668 (tp40) cc_final: 0.6926 (tt0) REVERT: A 221 MET cc_start: 0.8382 (ttm) cc_final: 0.8060 (ttp) REVERT: A 299 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: B 217 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7027 (ppp) REVERT: N 87 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8238 (mttm) REVERT: N 106 ASP cc_start: 0.7312 (p0) cc_final: 0.7085 (p0) outliers start: 36 outliers final: 11 residues processed: 179 average time/residue: 0.4797 time to fit residues: 93.2446 Evaluate side-chains 152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 372 ILE 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 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 12 GLN A 41 HIS 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 = 0.3927 r_free = 0.3927 target = 0.165877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132259 restraints weight = 11619.633| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.64 r_work: 0.3395 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10025 Z= 0.279 Angle : 0.649 8.202 13605 Z= 0.338 Chirality : 0.046 0.220 1518 Planarity : 0.005 0.040 1724 Dihedral : 7.626 59.937 1587 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.17 % Allowed : 18.82 % Favored : 77.01 % 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: -0.89 (0.23), residues: 1230 helix: 0.10 (0.23), residues: 492 sheet: -1.25 (0.32), residues: 224 loop : -0.79 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 67 TYR 0.020 0.002 TYR A 358 PHE 0.024 0.002 PHE R 359 TRP 0.019 0.002 TRP R 236 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00637 (10014) covalent geometry : angle 0.64590 (13584) SS BOND : bond 0.00662 ( 9) SS BOND : angle 1.65939 ( 18) hydrogen bonds : bond 0.04329 ( 468) hydrogen bonds : angle 5.49353 ( 1320) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00303 ( 1) link_NAG-ASN : angle 1.59500 ( 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 173 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.338 Fit side-chains REVERT: E 103 PHE cc_start: 0.6579 (m-10) cc_final: 0.6145 (m-80) REVERT: R 49 MET cc_start: 0.7810 (mmm) cc_final: 0.6783 (mpp) REVERT: R 52 GLN cc_start: 0.7686 (tt0) cc_final: 0.7113 (tt0) REVERT: R 77 ASP cc_start: 0.7824 (p0) cc_final: 0.7516 (p0) REVERT: R 143 LYS cc_start: 0.7052 (tttt) cc_final: 0.6299 (mtmt) REVERT: R 306 MET cc_start: 0.8567 (mmm) cc_final: 0.8363 (mmt) REVERT: R 321 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7112 (ttm170) REVERT: R 373 ASP cc_start: 0.7882 (m-30) cc_final: 0.7664 (m-30) REVERT: R 405 GLN cc_start: 0.6423 (mp10) cc_final: 0.6216 (mp10) REVERT: A 31 GLN cc_start: 0.7553 (tp40) cc_final: 0.6899 (tt0) REVERT: A 221 MET cc_start: 0.8277 (ttm) cc_final: 0.7870 (ttp) REVERT: A 299 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6203 (tt0) REVERT: A 372 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 59 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7283 (t80) REVERT: B 130 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4763 (mp0) REVERT: B 217 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7352 (ttt) REVERT: N 1 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7152 (tt0) outliers start: 41 outliers final: 21 residues processed: 162 average time/residue: 0.5127 time to fit residues: 90.0253 Evaluate side-chains 153 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 R residue 375 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 A residue 372 ILE 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 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER 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 113 THR Chi-restraints excluded: chain N residue 114 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: 0.9980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN A 12 GLN A 236 GLN A 357 HIS N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137699 restraints weight = 11389.329| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.73 r_work: 0.3449 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10025 Z= 0.124 Angle : 0.522 7.900 13605 Z= 0.273 Chirality : 0.041 0.162 1518 Planarity : 0.003 0.050 1724 Dihedral : 6.913 58.661 1587 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.66 % Allowed : 21.26 % Favored : 75.08 % 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: -0.53 (0.24), residues: 1230 helix: 0.53 (0.24), residues: 498 sheet: -1.25 (0.32), residues: 227 loop : -0.65 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.018 0.001 TYR R 284 PHE 0.014 0.001 PHE R 119 TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00276 (10014) covalent geometry : angle 0.51939 (13584) SS BOND : bond 0.00551 ( 9) SS BOND : angle 1.26322 ( 18) hydrogen bonds : bond 0.03588 ( 468) hydrogen bonds : angle 4.94693 ( 1320) Misc. bond : bond 0.00025 ( 1) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 1.59375 ( 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 183 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.421 Fit side-chains REVERT: E 103 PHE cc_start: 0.6470 (m-80) cc_final: 0.5995 (m-80) REVERT: R 49 MET cc_start: 0.7833 (mmm) cc_final: 0.6404 (mpp) REVERT: R 52 GLN cc_start: 0.7694 (tt0) cc_final: 0.7052 (tm-30) REVERT: R 77 ASP cc_start: 0.7769 (p0) cc_final: 0.7488 (p0) REVERT: R 143 LYS cc_start: 0.7038 (tttt) cc_final: 0.6304 (mtmt) REVERT: R 321 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6733 (ttm170) REVERT: R 373 ASP cc_start: 0.7833 (m-30) cc_final: 0.7564 (m-30) REVERT: A 31 GLN cc_start: 0.7546 (tp40) cc_final: 0.6909 (tt0) REVERT: A 221 MET cc_start: 0.8267 (ttm) cc_final: 0.7815 (ttp) REVERT: A 299 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6214 (tt0) REVERT: B 217 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7375 (ppp) REVERT: N 1 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7156 (tt0) outliers start: 36 outliers final: 17 residues processed: 172 average time/residue: 0.4975 time to fit residues: 92.9303 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 : 0.357 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 305 VAL 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 369 THR Chi-restraints excluded: chain B residue 112 VAL 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 31 ASN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 12 GLN A 41 HIS A 279 ASN A 357 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137707 restraints weight = 11514.075| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.79 r_work: 0.3452 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10025 Z= 0.126 Angle : 0.520 8.351 13605 Z= 0.272 Chirality : 0.041 0.206 1518 Planarity : 0.003 0.052 1724 Dihedral : 6.755 56.065 1587 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.56 % Allowed : 22.18 % Favored : 74.26 % 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: -0.38 (0.24), residues: 1230 helix: 0.70 (0.24), residues: 501 sheet: -1.18 (0.33), residues: 227 loop : -0.63 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.019 0.001 TYR R 372 PHE 0.011 0.001 PHE R 119 TRP 0.015 0.001 TRP B 169 HIS 0.009 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00282 (10014) covalent geometry : angle 0.51839 (13584) SS BOND : bond 0.00507 ( 9) SS BOND : angle 1.13284 ( 18) hydrogen bonds : bond 0.03474 ( 468) hydrogen bonds : angle 4.79915 ( 1320) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 1.50863 ( 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 167 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.231 Fit side-chains REVERT: E 103 PHE cc_start: 0.6408 (m-80) cc_final: 0.5951 (m-80) REVERT: R 49 MET cc_start: 0.7815 (mmm) cc_final: 0.6397 (mpp) REVERT: R 52 GLN cc_start: 0.7632 (tt0) cc_final: 0.7003 (tm-30) REVERT: R 77 ASP cc_start: 0.7775 (p0) cc_final: 0.7514 (p0) REVERT: R 143 LYS cc_start: 0.7034 (tttt) cc_final: 0.6296 (mtmt) REVERT: R 321 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6751 (ttm170) REVERT: R 346 MET cc_start: 0.7437 (mmp) cc_final: 0.6350 (ptp) REVERT: R 373 ASP cc_start: 0.7836 (m-30) cc_final: 0.7532 (m-30) REVERT: A 31 GLN cc_start: 0.7475 (tp40) cc_final: 0.6787 (tt0) REVERT: A 221 MET cc_start: 0.8239 (ttm) cc_final: 0.7888 (ttp) REVERT: A 299 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6241 (tt0) REVERT: B 217 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7298 (ppp) outliers start: 35 outliers final: 20 residues processed: 155 average time/residue: 0.4552 time to fit residues: 76.8191 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 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 92 TYR 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 346 LEU 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 112 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN A 12 GLN A 279 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.165796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131532 restraints weight = 11457.376| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.79 r_work: 0.3383 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10025 Z= 0.253 Angle : 0.625 9.202 13605 Z= 0.325 Chirality : 0.045 0.212 1518 Planarity : 0.004 0.048 1724 Dihedral : 7.518 55.441 1587 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.66 % Allowed : 22.08 % Favored : 74.26 % 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: -0.55 (0.24), residues: 1230 helix: 0.52 (0.23), residues: 491 sheet: -1.33 (0.32), residues: 230 loop : -0.62 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 232 TYR 0.027 0.002 TYR R 284 PHE 0.012 0.002 PHE A 212 TRP 0.016 0.002 TRP R 236 HIS 0.009 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00576 (10014) covalent geometry : angle 0.62174 (13584) SS BOND : bond 0.00610 ( 9) SS BOND : angle 1.61076 ( 18) hydrogen bonds : bond 0.04022 ( 468) hydrogen bonds : angle 5.19549 ( 1320) Misc. bond : bond 0.00025 ( 1) link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 1.82809 ( 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 163 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.430 Fit side-chains REVERT: E 103 PHE cc_start: 0.6310 (m-80) cc_final: 0.5864 (m-80) REVERT: R 49 MET cc_start: 0.7816 (mmm) cc_final: 0.6296 (mpp) REVERT: R 77 ASP cc_start: 0.7810 (p0) cc_final: 0.7512 (p0) REVERT: R 143 LYS cc_start: 0.7030 (tttt) cc_final: 0.6252 (mtmt) REVERT: R 321 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7089 (ttm170) REVERT: R 373 ASP cc_start: 0.7890 (m-30) cc_final: 0.7642 (m-30) REVERT: A 31 GLN cc_start: 0.7415 (tp40) cc_final: 0.6724 (tt0) REVERT: A 221 MET cc_start: 0.8288 (ttm) cc_final: 0.7874 (ttp) REVERT: A 299 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6188 (tt0) REVERT: B 59 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7215 (t80) REVERT: B 217 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7351 (ppp) REVERT: N 1 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7065 (tt0) outliers start: 36 outliers final: 20 residues processed: 151 average time/residue: 0.5460 time to fit residues: 89.3883 Evaluate side-chains 149 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 346 LEU Chi-restraints excluded: chain A residue 369 THR 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 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 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 GLN R 399 GLN A 12 GLN A 279 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137052 restraints weight = 11421.968| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.73 r_work: 0.3442 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10025 Z= 0.128 Angle : 0.532 9.207 13605 Z= 0.276 Chirality : 0.041 0.173 1518 Planarity : 0.004 0.054 1724 Dihedral : 6.966 54.368 1587 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.36 % Allowed : 22.79 % Favored : 73.86 % 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: -0.32 (0.24), residues: 1230 helix: 0.73 (0.23), residues: 500 sheet: -1.22 (0.33), residues: 227 loop : -0.53 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.021 0.001 TYR R 372 PHE 0.010 0.001 PHE A 222 TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00285 (10014) covalent geometry : angle 0.52971 (13584) SS BOND : bond 0.00423 ( 9) SS BOND : angle 1.30715 ( 18) hydrogen bonds : bond 0.03477 ( 468) hydrogen bonds : angle 4.88633 ( 1320) Misc. bond : bond 0.00019 ( 1) link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.77868 ( 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 165 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.280 Fit side-chains REVERT: E 103 PHE cc_start: 0.6259 (m-80) cc_final: 0.5796 (m-80) REVERT: R 49 MET cc_start: 0.7771 (mmm) cc_final: 0.6452 (mpp) REVERT: R 77 ASP cc_start: 0.7866 (p0) cc_final: 0.7611 (p0) REVERT: R 137 PHE cc_start: 0.7134 (m-80) cc_final: 0.6933 (m-80) REVERT: R 143 LYS cc_start: 0.6995 (tttt) cc_final: 0.6298 (mtmt) REVERT: R 321 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6850 (ttm170) REVERT: R 346 MET cc_start: 0.7466 (mmp) cc_final: 0.6329 (ttp) REVERT: R 405 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: A 31 GLN cc_start: 0.7482 (tp40) cc_final: 0.6832 (tt0) REVERT: A 221 MET cc_start: 0.8226 (ttm) cc_final: 0.7878 (ttp) REVERT: A 299 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6248 (tt0) REVERT: A 334 VAL cc_start: 0.7773 (t) cc_final: 0.7495 (p) REVERT: B 130 GLU cc_start: 0.5169 (OUTLIER) cc_final: 0.4714 (mp0) REVERT: B 217 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7392 (ppp) outliers start: 33 outliers final: 17 residues processed: 153 average time/residue: 0.5690 time to fit residues: 93.3544 Evaluate side-chains 145 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 R residue 405 GLN 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 B residue 112 VAL 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 G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 114 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN A 12 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138818 restraints weight = 11389.192| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.69 r_work: 0.3474 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10025 Z= 0.118 Angle : 0.531 9.004 13605 Z= 0.273 Chirality : 0.041 0.165 1518 Planarity : 0.004 0.055 1724 Dihedral : 6.655 55.654 1587 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.15 % Allowed : 23.09 % Favored : 73.75 % 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: 0.96 (0.24), residues: 503 sheet: -1.07 (0.33), residues: 229 loop : -0.46 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 214 TYR 0.019 0.001 TYR R 372 PHE 0.011 0.001 PHE A 222 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00265 (10014) covalent geometry : angle 0.52947 (13584) SS BOND : bond 0.00409 ( 9) SS BOND : angle 1.22885 ( 18) hydrogen bonds : bond 0.03324 ( 468) hydrogen bonds : angle 4.67971 ( 1320) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 1.63533 ( 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 169 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.379 Fit side-chains REVERT: E 103 PHE cc_start: 0.6263 (m-80) cc_final: 0.5763 (m-80) REVERT: R 49 MET cc_start: 0.7762 (mmm) cc_final: 0.6492 (mpp) REVERT: R 77 ASP cc_start: 0.7876 (p0) cc_final: 0.7625 (p0) REVERT: R 106 GLU cc_start: 0.4046 (mp0) cc_final: 0.3525 (mm-30) REVERT: R 137 PHE cc_start: 0.7188 (m-80) cc_final: 0.6639 (p90) REVERT: R 143 LYS cc_start: 0.6960 (tttt) cc_final: 0.6250 (mtmt) REVERT: R 158 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7117 (tp) REVERT: R 321 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6736 (ttm170) REVERT: R 346 MET cc_start: 0.7399 (mmp) cc_final: 0.6336 (ptp) REVERT: R 405 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6608 (mp10) REVERT: A 31 GLN cc_start: 0.7501 (tp40) cc_final: 0.6865 (tt0) REVERT: A 221 MET cc_start: 0.8168 (ttm) cc_final: 0.7932 (ttp) REVERT: A 299 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6279 (tt0) REVERT: A 334 VAL cc_start: 0.7760 (t) cc_final: 0.7500 (p) REVERT: A 346 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7406 (mt) REVERT: B 130 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4696 (mp0) REVERT: B 214 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7609 (mmt-90) REVERT: B 217 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7403 (ppp) outliers start: 31 outliers final: 15 residues processed: 156 average time/residue: 0.4632 time to fit residues: 78.3695 Evaluate side-chains 154 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 158 LEU 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 405 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 112 VAL 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 G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136261 restraints weight = 11401.391| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.74 r_work: 0.3435 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10025 Z= 0.159 Angle : 0.557 8.672 13605 Z= 0.289 Chirality : 0.042 0.186 1518 Planarity : 0.004 0.057 1724 Dihedral : 6.849 58.819 1587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.34 % Allowed : 23.91 % Favored : 73.75 % 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: -0.14 (0.24), residues: 1230 helix: 0.93 (0.23), residues: 500 sheet: -1.24 (0.32), residues: 236 loop : -0.40 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 214 TYR 0.016 0.001 TYR A 358 PHE 0.009 0.001 PHE A 212 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00362 (10014) covalent geometry : angle 0.55366 (13584) SS BOND : bond 0.00442 ( 9) SS BOND : angle 1.50506 ( 18) hydrogen bonds : bond 0.03486 ( 468) hydrogen bonds : angle 4.76402 ( 1320) Misc. bond : bond 0.00015 ( 1) link_NAG-ASN : bond 0.00014 ( 1) link_NAG-ASN : angle 1.84814 ( 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 150 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.279 Fit side-chains REVERT: E 103 PHE cc_start: 0.6263 (m-80) cc_final: 0.5795 (m-80) REVERT: R 49 MET cc_start: 0.7781 (mmm) cc_final: 0.6374 (mpp) REVERT: R 77 ASP cc_start: 0.7918 (p0) cc_final: 0.7691 (p0) REVERT: R 106 GLU cc_start: 0.4073 (mp0) cc_final: 0.3837 (mm-30) REVERT: R 143 LYS cc_start: 0.7043 (tttt) cc_final: 0.6344 (mtmt) REVERT: R 158 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7140 (tp) REVERT: R 306 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.8013 (mmm) REVERT: R 321 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6974 (ttm170) REVERT: R 373 ASP cc_start: 0.7880 (m-30) cc_final: 0.7556 (m-30) REVERT: R 405 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: A 31 GLN cc_start: 0.7493 (tp40) cc_final: 0.6832 (tt0) REVERT: A 221 MET cc_start: 0.8171 (ttm) cc_final: 0.7911 (ttp) REVERT: A 299 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6290 (tt0) REVERT: B 130 GLU cc_start: 0.5161 (OUTLIER) cc_final: 0.4703 (mp0) REVERT: B 217 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7403 (ppp) REVERT: N 106 ASP cc_start: 0.8088 (p0) cc_final: 0.7840 (p0) outliers start: 23 outliers final: 13 residues processed: 142 average time/residue: 0.5076 time to fit residues: 77.9459 Evaluate side-chains 144 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 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 158 LEU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 405 GLN 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 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 G residue 9 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.171210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138371 restraints weight = 11445.294| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.71 r_work: 0.3471 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10025 Z= 0.121 Angle : 0.533 8.705 13605 Z= 0.275 Chirality : 0.041 0.218 1518 Planarity : 0.004 0.059 1724 Dihedral : 6.638 59.142 1587 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.75 % Allowed : 23.70 % 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: 0.01 (0.24), residues: 1230 helix: 1.03 (0.23), residues: 509 sheet: -1.16 (0.33), residues: 229 loop : -0.33 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 214 TYR 0.024 0.001 TYR R 284 PHE 0.009 0.001 PHE A 212 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00271 (10014) covalent geometry : angle 0.53028 (13584) SS BOND : bond 0.00384 ( 9) SS BOND : angle 1.26654 ( 18) hydrogen bonds : bond 0.03329 ( 468) hydrogen bonds : angle 4.62575 ( 1320) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 1.77264 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.92 seconds wall clock time: 63 minutes 45.05 seconds (3825.05 seconds total)