Starting phenix.real_space_refine on Fri Sep 11 10:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.cif" model { file = "/net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oij_20078/09_2026/6oij_20078.map" } resolution = 3.3 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 59 5.16 5 C 5697 2.51 5 N 1500 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8877 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1781 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2273 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1757 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'IXO': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.59, per 1000 atoms: 0.18 Number of scatterers: 8877 At special positions: 0 Unit cell: (106, 117.66, 107.06, 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 59 16.00 O 1621 8.00 N 1500 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 313.6 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 37 removed outlier: 3.835A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.072A pdb=" N TRP A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.573A pdb=" N GLU A 221 " --> pdb=" O HIS A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 336 through 356 Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.852A pdb=" N TYR R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 89 removed outlier: 3.543A pdb=" N MET R 88 " --> pdb=" O THR R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 168 removed outlier: 4.011A pdb=" N SER R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Proline residue: R 159 - end of helix removed outlier: 3.508A pdb=" N LEU R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.126A pdb=" N LEU R 183 " --> pdb=" O ILE R 180 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER R 184 " --> pdb=" O GLN R 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 180 through 184' Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.577A pdb=" N THR R 189 " --> pdb=" O GLN R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 226 removed outlier: 4.413A pdb=" N ARG R 220 " --> pdb=" O GLU R 216 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU R 221 " --> pdb=" O ASN R 217 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 389 removed outlier: 3.910A pdb=" N ARG R 365 " --> pdb=" O LYS R 361 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 397 through 414 removed outlier: 4.258A pdb=" N CYS R 407 " --> pdb=" O GLY R 403 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR R 408 " --> pdb=" O TYR R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 419 removed outlier: 3.799A pdb=" N TYR R 418 " --> pdb=" O ASN R 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 432 Processing helix chain 'R' and resid 438 through 442 removed outlier: 3.542A pdb=" N TRP R 442 " --> pdb=" O LYS R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 22 removed outlier: 4.391A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 5.871A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 229 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.850A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.790A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.883A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.276A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.718A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.525A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.984A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.640A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1299 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: 1.03 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.44: 2541 1.44 - 1.56: 5037 1.56 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 9074 Sorted by residual: bond pdb=" C GLU H 234 " pdb=" N TYR H 235 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.46e+01 bond pdb=" N11 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.385 1.425 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.310 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C ASP H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.61e+00 bond pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.50e+00 ... (remaining 9069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11965 2.30 - 4.59: 328 4.59 - 6.89: 33 6.89 - 9.19: 12 9.19 - 11.48: 10 Bond angle restraints: 12348 Sorted by residual: angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 122.61 129.80 -7.19 1.56e+00 4.11e-01 2.13e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 108.34 113.73 -5.39 1.31e+00 5.83e-01 1.69e+01 angle pdb=" C TYR R 82 " pdb=" N THR R 83 " pdb=" CA THR R 83 " ideal model delta sigma weight residual 121.14 114.52 6.62 1.75e+00 3.27e-01 1.43e+01 angle pdb=" CA MET H 192 " pdb=" CB MET H 192 " pdb=" CG MET H 192 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N THR R 379 " pdb=" CA THR R 379 " pdb=" C THR R 379 " ideal model delta sigma weight residual 109.81 117.17 -7.36 2.21e+00 2.05e-01 1.11e+01 ... (remaining 12343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 4976 24.20 - 48.40: 294 48.40 - 72.61: 31 72.61 - 96.81: 5 96.81 - 121.01: 1 Dihedral angle restraints: 5307 sinusoidal: 1963 harmonic: 3344 Sorted by residual: dihedral pdb=" CA GLU A 234 " pdb=" C GLU A 234 " pdb=" N TYR A 235 " pdb=" CA TYR A 235 " ideal model delta harmonic sigma weight residual 180.00 149.44 30.56 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 888 0.044 - 0.089: 368 0.089 - 0.133: 136 0.133 - 0.178: 24 0.178 - 0.222: 8 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE R 180 " pdb=" CA ILE R 180 " pdb=" CG1 ILE R 180 " pdb=" CG2 ILE R 180 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE A 200 " pdb=" CA ILE A 200 " pdb=" CG1 ILE A 200 " pdb=" CG2 ILE A 200 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1421 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 236 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 414 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO R 415 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 83 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C THR R 83 " -0.041 2.00e-02 2.50e+03 pdb=" O THR R 83 " 0.015 2.00e-02 2.50e+03 pdb=" N THR R 84 " 0.014 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1689 2.77 - 3.30: 7932 3.30 - 3.83: 14902 3.83 - 4.37: 16879 4.37 - 4.90: 30037 Nonbonded interactions: 71439 Sorted by model distance: nonbonded pdb=" OG1 THR R 377 " pdb=" O LEU R 406 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.266 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.280 3.040 nonbonded pdb=" O LEU R 81 " pdb=" OG1 THR R 84 " model vdw 2.287 3.040 ... (remaining 71434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.006 0.079 9077 Z= 0.270 Angle : 0.943 11.484 12354 Z= 0.501 Chirality : 0.057 0.222 1424 Planarity : 0.007 0.082 1540 Dihedral : 15.285 121.011 3142 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.77 % Allowed : 12.72 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.70 (0.20), residues: 1134 helix: -2.41 (0.19), residues: 395 sheet: -1.87 (0.30), residues: 238 loop : -2.67 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.018 0.002 TYR R 404 PHE 0.022 0.002 PHE R 182 TRP 0.032 0.003 TRP R 91 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 ( 9074) covalent geometry : angle 0.94199 / 0.50 (12348) SS BOND : bond 0.00464 / 0.23 ( 3) SS BOND : angle 1.72053 / 0.88 ( 6) hydrogen bonds : bond 0.14394 / 9.63 ( 441) hydrogen bonds : angle 6.90123 / 4.74 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8503 (tptp) cc_final: 0.7979 (ttpt) REVERT: A 357 ASN cc_start: 0.8445 (t0) cc_final: 0.7799 (t0) REVERT: R 404 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6507 (m-10) REVERT: H 5 VAL cc_start: 0.8470 (m) cc_final: 0.8194 (t) REVERT: H 148 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8032 (Cg_exo) REVERT: H 192 MET cc_start: 0.8501 (ppp) cc_final: 0.8206 (ppp) REVERT: H 246 GLU cc_start: 0.7377 (mp0) cc_final: 0.7048 (mp0) REVERT: G 48 ASP cc_start: 0.8329 (t0) cc_final: 0.8097 (t0) outliers start: 7 outliers final: 2 residues processed: 214 average time/residue: 0.1028 time to fit residues: 30.2265 Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 GLN A 274 ASN A 287 HIS R 43 ASN R 61 ASN R 90 HIS R 382 ASN R 410 ASN H 142 GLN H 183 GLN B 75 GLN B 88 ASN B 239 ASN B 266 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105248 restraints weight = 13490.656| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.34 r_work: 0.3114 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9077 Z= 0.147 Angle : 0.628 7.563 12354 Z= 0.324 Chirality : 0.043 0.244 1424 Planarity : 0.005 0.064 1540 Dihedral : 7.654 113.002 1283 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.54 % Allowed : 17.15 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.96 (0.23), residues: 1134 helix: -0.21 (0.24), residues: 393 sheet: -1.35 (0.31), residues: 246 loop : -2.15 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.015 0.001 TYR H 227 PHE 0.015 0.001 PHE A 55 TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9074) covalent geometry : angle 0.62732 / 0.32 (12348) SS BOND : bond 0.00310 / 0.15 ( 3) SS BOND : angle 1.30862 / 0.69 ( 6) hydrogen bonds : bond 0.04126 / 2.78 ( 441) hydrogen bonds : angle 4.77939 / 3.29 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.361 Fit side-chains REVERT: A 258 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 294 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7114 (pm20) REVERT: A 311 LYS cc_start: 0.8780 (tptp) cc_final: 0.8233 (ttpt) REVERT: A 329 THR cc_start: 0.8490 (p) cc_final: 0.8228 (t) REVERT: R 23 TRP cc_start: 0.7312 (p-90) cc_final: 0.6956 (p-90) REVERT: R 217 ASN cc_start: 0.8471 (t0) cc_final: 0.8130 (t0) REVERT: H 18 ARG cc_start: 0.7237 (tpp80) cc_final: 0.7014 (tpt-90) REVERT: H 148 PRO cc_start: 0.8611 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: H 227 TYR cc_start: 0.8338 (m-10) cc_final: 0.8006 (m-80) REVERT: H 246 GLU cc_start: 0.7221 (mp0) cc_final: 0.7008 (mp0) REVERT: G 21 MET cc_start: 0.8392 (ttp) cc_final: 0.8129 (tpp) REVERT: G 48 ASP cc_start: 0.8553 (t0) cc_final: 0.8151 (t0) outliers start: 32 outliers final: 17 residues processed: 205 average time/residue: 0.0869 time to fit residues: 25.7680 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 0.0970 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS R 422 ASN H 39 GLN H 142 GLN H 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103384 restraints weight = 13714.240| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.18 r_work: 0.3103 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.150 Angle : 0.629 8.797 12354 Z= 0.321 Chirality : 0.044 0.213 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.418 113.129 1283 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.10 % Allowed : 20.24 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.25 (0.24), residues: 1134 helix: 0.67 (0.26), residues: 393 sheet: -1.11 (0.32), residues: 245 loop : -1.91 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.013 0.001 TYR G 40 PHE 0.012 0.001 PHE A 339 TRP 0.026 0.001 TRP B 82 HIS 0.009 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9074) covalent geometry : angle 0.62792 / 0.32 (12348) SS BOND : bond 0.00552 / 0.27 ( 3) SS BOND : angle 1.75359 / 0.92 ( 6) hydrogen bonds : bond 0.03836 / 2.60 ( 441) hydrogen bonds : angle 4.55518 / 3.14 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 222 ASN cc_start: 0.8090 (t0) cc_final: 0.7564 (p0) REVERT: A 258 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 311 LYS cc_start: 0.8826 (tptp) cc_final: 0.8268 (ttpt) REVERT: A 329 THR cc_start: 0.8536 (p) cc_final: 0.8331 (t) REVERT: R 23 TRP cc_start: 0.7258 (p-90) cc_final: 0.6902 (p-90) REVERT: H 18 ARG cc_start: 0.7304 (tpp80) cc_final: 0.7081 (tpt-90) REVERT: H 148 PRO cc_start: 0.8607 (Cg_endo) cc_final: 0.8269 (Cg_exo) REVERT: H 227 TYR cc_start: 0.8334 (m-10) cc_final: 0.7980 (m-80) REVERT: G 48 ASP cc_start: 0.8470 (t0) cc_final: 0.8177 (t0) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.0884 time to fit residues: 23.3234 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN B 156 GLN G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102904 restraints weight = 14044.100| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.29 r_work: 0.3081 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9077 Z= 0.185 Angle : 0.642 7.785 12354 Z= 0.327 Chirality : 0.045 0.220 1424 Planarity : 0.004 0.059 1540 Dihedral : 7.334 112.562 1283 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.76 % Allowed : 21.13 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.00 (0.24), residues: 1134 helix: 0.97 (0.26), residues: 393 sheet: -1.13 (0.32), residues: 253 loop : -1.75 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.012 0.001 TYR B 105 PHE 0.014 0.001 PHE A 341 TRP 0.025 0.001 TRP B 82 HIS 0.008 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 9074) covalent geometry : angle 0.64050 / 0.33 (12348) SS BOND : bond 0.00652 / 0.32 ( 3) SS BOND : angle 2.13919 / 1.13 ( 6) hydrogen bonds : bond 0.03894 / 2.63 ( 441) hydrogen bonds : angle 4.53490 / 3.12 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 222 ASN cc_start: 0.8054 (t0) cc_final: 0.7516 (p0) REVERT: A 249 GLU cc_start: 0.7841 (tp30) cc_final: 0.7543 (tp30) REVERT: A 301 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7623 (t0) REVERT: A 311 LYS cc_start: 0.8837 (tptp) cc_final: 0.8253 (ttpt) REVERT: A 329 THR cc_start: 0.8577 (p) cc_final: 0.8376 (t) REVERT: R 23 TRP cc_start: 0.7266 (p-90) cc_final: 0.6892 (p-90) REVERT: H 227 TYR cc_start: 0.8397 (m-10) cc_final: 0.8041 (m-80) REVERT: B 156 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: G 18 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: G 22 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7518 (mt-10) outliers start: 34 outliers final: 22 residues processed: 188 average time/residue: 0.0903 time to fit residues: 24.0895 Evaluate side-chains 174 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103989 restraints weight = 13947.734| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.151 Angle : 0.613 7.105 12354 Z= 0.313 Chirality : 0.044 0.199 1424 Planarity : 0.004 0.059 1540 Dihedral : 7.134 112.961 1282 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.87 % Allowed : 21.68 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.78 (0.24), residues: 1134 helix: 1.19 (0.26), residues: 392 sheet: -1.05 (0.32), residues: 248 loop : -1.63 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.013 0.001 TYR G 40 PHE 0.011 0.001 PHE A 339 TRP 0.023 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9074) covalent geometry : angle 0.61204 / 0.31 (12348) SS BOND : bond 0.00585 / 0.28 ( 3) SS BOND : angle 1.46897 / 0.78 ( 6) hydrogen bonds : bond 0.03691 / 2.49 ( 441) hydrogen bonds : angle 4.44519 / 3.07 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.337 Fit side-chains REVERT: A 221 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 222 ASN cc_start: 0.7979 (t0) cc_final: 0.7477 (p0) REVERT: A 294 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7181 (pm20) REVERT: A 301 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7588 (t0) REVERT: A 307 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7546 (mt-10) REVERT: R 23 TRP cc_start: 0.7217 (p-90) cc_final: 0.6893 (p-90) REVERT: R 372 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7790 (tt) REVERT: H 11 LEU cc_start: 0.7479 (tp) cc_final: 0.7223 (mp) REVERT: H 227 TYR cc_start: 0.8388 (m-10) cc_final: 0.8035 (m-80) REVERT: B 156 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: B 247 ASP cc_start: 0.9018 (p0) cc_final: 0.8745 (p0) REVERT: G 22 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7642 (mp0) outliers start: 35 outliers final: 22 residues processed: 188 average time/residue: 0.0898 time to fit residues: 24.0393 Evaluate side-chains 173 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104964 restraints weight = 13727.693| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.36 r_work: 0.3112 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9077 Z= 0.132 Angle : 0.605 7.047 12354 Z= 0.309 Chirality : 0.043 0.163 1424 Planarity : 0.004 0.059 1540 Dihedral : 6.845 113.437 1282 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.20 % Allowed : 22.35 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.58 (0.25), residues: 1134 helix: 1.34 (0.27), residues: 393 sheet: -0.95 (0.32), residues: 252 loop : -1.49 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.009 0.001 TYR H 103 PHE 0.012 0.001 PHE A 255 TRP 0.023 0.001 TRP B 82 HIS 0.008 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9074) covalent geometry : angle 0.60264 / 0.31 (12348) SS BOND : bond 0.00532 / 0.26 ( 3) SS BOND : angle 2.29289 / 1.21 ( 6) hydrogen bonds : bond 0.03540 / 2.38 ( 441) hydrogen bonds : angle 4.32761 / 2.99 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.353 Fit side-chains REVERT: A 221 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 222 ASN cc_start: 0.7862 (t0) cc_final: 0.7468 (p0) REVERT: A 301 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7731 (t0) REVERT: R 23 TRP cc_start: 0.7223 (p-90) cc_final: 0.6881 (p-90) REVERT: R 372 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7753 (tt) REVERT: H 194 ASN cc_start: 0.8596 (m-40) cc_final: 0.8377 (m-40) REVERT: H 220 GLU cc_start: 0.7571 (pm20) cc_final: 0.7363 (pm20) REVERT: H 227 TYR cc_start: 0.8368 (m-10) cc_final: 0.8005 (m-80) REVERT: B 156 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: B 338 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8800 (mm) REVERT: G 22 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7617 (mp0) outliers start: 38 outliers final: 26 residues processed: 196 average time/residue: 0.0822 time to fit residues: 23.1948 Evaluate side-chains 185 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN B 6 GLN B 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104925 restraints weight = 13870.622| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.32 r_work: 0.3106 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9077 Z= 0.144 Angle : 0.609 7.133 12354 Z= 0.311 Chirality : 0.044 0.289 1424 Planarity : 0.004 0.058 1540 Dihedral : 6.764 113.432 1282 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.09 % Allowed : 22.68 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.50 (0.25), residues: 1134 helix: 1.36 (0.26), residues: 393 sheet: -0.87 (0.32), residues: 247 loop : -1.44 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.015 0.001 TYR G 40 PHE 0.011 0.001 PHE A 339 TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9074) covalent geometry : angle 0.60729 / 0.31 (12348) SS BOND : bond 0.00557 / 0.27 ( 3) SS BOND : angle 1.98295 / 1.04 ( 6) hydrogen bonds : bond 0.03568 / 2.39 ( 441) hydrogen bonds : angle 4.31093 / 2.98 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.222 Fit side-chains REVERT: A 221 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 222 ASN cc_start: 0.7854 (t0) cc_final: 0.7440 (p0) REVERT: A 301 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7699 (t0) REVERT: R 23 TRP cc_start: 0.7145 (p-90) cc_final: 0.6789 (p-90) REVERT: R 372 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7780 (tt) REVERT: H 194 ASN cc_start: 0.8616 (m-40) cc_final: 0.8405 (m-40) REVERT: H 220 GLU cc_start: 0.7451 (pm20) cc_final: 0.7169 (pm20) REVERT: H 227 TYR cc_start: 0.8360 (m-10) cc_final: 0.8040 (m-80) REVERT: B 156 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: B 338 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8821 (mm) REVERT: G 22 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7661 (mp0) outliers start: 46 outliers final: 34 residues processed: 197 average time/residue: 0.0853 time to fit residues: 24.2269 Evaluate side-chains 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 398 THR Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104918 restraints weight = 13716.166| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.30 r_work: 0.3118 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.131 Angle : 0.616 9.306 12354 Z= 0.314 Chirality : 0.044 0.244 1424 Planarity : 0.004 0.058 1540 Dihedral : 6.674 113.646 1282 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.76 % Allowed : 23.01 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.43 (0.25), residues: 1134 helix: 1.38 (0.27), residues: 393 sheet: -0.81 (0.32), residues: 247 loop : -1.36 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.009 0.001 TYR A 235 PHE 0.011 0.001 PHE A 255 TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9074) covalent geometry : angle 0.61455 / 0.31 (12348) SS BOND : bond 0.00525 / 0.25 ( 3) SS BOND : angle 1.74697 / 0.92 ( 6) hydrogen bonds : bond 0.03543 / 2.37 ( 441) hydrogen bonds : angle 4.28660 / 2.97 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.343 Fit side-chains REVERT: A 203 MET cc_start: 0.8486 (ttp) cc_final: 0.8182 (ttm) REVERT: A 221 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 222 ASN cc_start: 0.7737 (t0) cc_final: 0.7454 (p0) REVERT: A 301 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7648 (t0) REVERT: R 23 TRP cc_start: 0.7120 (p-90) cc_final: 0.6785 (p-90) REVERT: R 217 ASN cc_start: 0.8310 (t0) cc_final: 0.8009 (t0) REVERT: R 372 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7767 (tt) REVERT: H 194 ASN cc_start: 0.8623 (m-40) cc_final: 0.8409 (m-40) REVERT: H 220 GLU cc_start: 0.7429 (pm20) cc_final: 0.7132 (pm20) REVERT: H 227 TYR cc_start: 0.8333 (m-10) cc_final: 0.8027 (m-80) REVERT: B 156 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: B 338 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8812 (mm) outliers start: 43 outliers final: 35 residues processed: 197 average time/residue: 0.0790 time to fit residues: 22.8239 Evaluate side-chains 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 398 THR Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 9.9990 chunk 73 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN B 156 GLN B 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105517 restraints weight = 13678.654| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.29 r_work: 0.3125 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9077 Z= 0.126 Angle : 0.613 9.004 12354 Z= 0.313 Chirality : 0.044 0.226 1424 Planarity : 0.004 0.058 1540 Dihedral : 6.593 113.840 1282 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.65 % Allowed : 22.79 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.34 (0.25), residues: 1134 helix: 1.41 (0.27), residues: 392 sheet: -0.70 (0.32), residues: 246 loop : -1.30 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.017 0.001 TYR G 40 PHE 0.015 0.001 PHE R 182 TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9074) covalent geometry : angle 0.61179 / 0.31 (12348) SS BOND : bond 0.00513 / 0.25 ( 3) SS BOND : angle 1.66223 / 0.88 ( 6) hydrogen bonds : bond 0.03488 / 2.33 ( 441) hydrogen bonds : angle 4.28135 / 2.96 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.308 Fit side-chains REVERT: A 203 MET cc_start: 0.8482 (ttp) cc_final: 0.8175 (ttm) REVERT: A 221 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 222 ASN cc_start: 0.7710 (t0) cc_final: 0.7441 (p0) REVERT: A 301 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7642 (t0) REVERT: R 23 TRP cc_start: 0.7116 (p-90) cc_final: 0.6763 (p-90) REVERT: R 217 ASN cc_start: 0.8311 (t0) cc_final: 0.8003 (t0) REVERT: R 372 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7743 (tt) REVERT: R 423 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8468 (ttpp) REVERT: H 194 ASN cc_start: 0.8618 (m-40) cc_final: 0.8418 (m-40) REVERT: H 220 GLU cc_start: 0.7476 (pm20) cc_final: 0.7191 (pm20) REVERT: H 227 TYR cc_start: 0.8315 (m-10) cc_final: 0.8004 (m-80) REVERT: B 129 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7605 (ttt90) REVERT: B 338 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (mm) outliers start: 42 outliers final: 32 residues processed: 198 average time/residue: 0.0877 time to fit residues: 24.5801 Evaluate side-chains 192 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 398 THR Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.0670 chunk 68 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS H 183 GLN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106325 restraints weight = 13661.400| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.30 r_work: 0.3140 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9077 Z= 0.115 Angle : 0.615 8.944 12354 Z= 0.312 Chirality : 0.043 0.264 1424 Planarity : 0.004 0.059 1540 Dihedral : 6.527 114.045 1282 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.31 % Allowed : 23.23 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.26 (0.25), residues: 1134 helix: 1.45 (0.27), residues: 392 sheet: -0.60 (0.32), residues: 244 loop : -1.26 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.009 0.001 TYR A 235 PHE 0.015 0.001 PHE R 182 TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9074) covalent geometry : angle 0.61388 / 0.31 (12348) SS BOND : bond 0.00482 / 0.23 ( 3) SS BOND : angle 1.57002 / 0.83 ( 6) hydrogen bonds : bond 0.03409 / 2.28 ( 441) hydrogen bonds : angle 4.27041 / 2.95 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.344 Fit side-chains REVERT: A 203 MET cc_start: 0.8457 (ttp) cc_final: 0.8136 (ttm) REVERT: A 221 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 258 ILE cc_start: 0.8787 (mt) cc_final: 0.8581 (mt) REVERT: A 301 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7544 (t0) REVERT: R 23 TRP cc_start: 0.6987 (p-90) cc_final: 0.6656 (p-90) REVERT: R 154 PHE cc_start: 0.8143 (t80) cc_final: 0.7940 (t80) REVERT: R 217 ASN cc_start: 0.8290 (t0) cc_final: 0.7985 (t0) REVERT: R 372 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8025 (tp) REVERT: R 423 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8412 (ttpp) REVERT: H 220 GLU cc_start: 0.7471 (pm20) cc_final: 0.7197 (pm20) REVERT: H 227 TYR cc_start: 0.8288 (m-10) cc_final: 0.7974 (m-80) REVERT: B 129 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7604 (ttt90) REVERT: B 247 ASP cc_start: 0.8724 (p0) cc_final: 0.8435 (p0) REVERT: B 338 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (mm) outliers start: 39 outliers final: 34 residues processed: 196 average time/residue: 0.0862 time to fit residues: 24.2597 Evaluate side-chains 196 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 372 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 398 THR Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105680 restraints weight = 13504.684| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.27 r_work: 0.3130 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.623 9077 Z= 0.347 Angle : 0.656 23.827 12354 Z= 0.330 Chirality : 0.043 0.264 1424 Planarity : 0.004 0.059 1540 Dihedral : 6.577 114.045 1282 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.20 % Allowed : 23.56 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.26 (0.25), residues: 1134 helix: 1.45 (0.27), residues: 392 sheet: -0.60 (0.32), residues: 244 loop : -1.26 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.009 0.001 TYR A 235 PHE 0.015 0.001 PHE R 182 TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9074) covalent geometry : angle 0.61559 / 0.31 (12348) SS BOND : bond 0.35985 / 18.94 ( 3) SS BOND : angle 10.30409 / 5.49 ( 6) hydrogen bonds : bond 0.03409 / 2.28 ( 441) hydrogen bonds : angle 4.27041 / 2.95 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.40 seconds wall clock time: 45 minutes 15.06 seconds (2715.06 seconds total)