Starting phenix.real_space_refine on Tue Mar 3 22:39:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oij_20078/03_2026/6oij_20078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oij_20078/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6oij_20078/03_2026/6oij_20078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oij_20078/03_2026/6oij_20078.map" model { file = "/net/cci-nas-00/data/ceres_data/6oij_20078/03_2026/6oij_20078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oij_20078/03_2026/6oij_20078.cif" } 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-dev-5986/lib/python3.9/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: 1.71, per 1000 atoms: 0.19 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: 0.65 Conformation dependent library (CDL) restraints added in 336.4 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: 0.18 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: 1.21 Time building geometry restraints manager: 0.89 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: 5080 24.20 - 48.40: 302 48.40 - 72.61: 35 72.61 - 96.81: 6 96.81 - 121.01: 4 Dihedral angle restraints: 5427 sinusoidal: 2083 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 5424 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.910 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 15.714 121.011 3262 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 covalent geometry : bond 0.00609 ( 9074) covalent geometry : angle 0.94199 (12348) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.72053 ( 6) hydrogen bonds : bond 0.14394 ( 441) hydrogen bonds : angle 6.90123 ( 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 : 0.328 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: 0.0944 time to fit residues: 27.5482 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 : 0.338 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 265 GLN A 274 ASN A 287 HIS R 43 ASN R 61 ASN R 90 HIS R 410 ASN H 142 GLN H 183 GLN B 75 GLN B 88 ASN B 239 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104740 restraints weight = 13496.663| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.23 r_work: 0.3111 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1530 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= 0.149 Angle : 0.644 7.950 12354 Z= 0.330 Chirality : 0.044 0.255 1424 Planarity : 0.005 0.065 1540 Dihedral : 8.096 76.021 1403 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.21 % Allowed : 17.15 % Favored : 79.65 % 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: -2.02 (0.23), residues: 1134 helix: -0.27 (0.24), residues: 393 sheet: -1.38 (0.31), residues: 246 loop : -2.16 (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 R 85 PHE 0.016 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 covalent geometry : bond 0.00332 ( 9074) covalent geometry : angle 0.64328 (12348) SS BOND : bond 0.00622 ( 3) SS BOND : angle 1.32867 ( 6) hydrogen bonds : bond 0.04248 ( 441) hydrogen bonds : angle 4.86838 ( 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 204 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 258 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8730 (mt) REVERT: A 294 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7099 (pm20) REVERT: A 311 LYS cc_start: 0.8768 (tptp) cc_final: 0.8203 (ttpt) REVERT: A 329 THR cc_start: 0.8487 (p) cc_final: 0.8216 (t) REVERT: R 23 TRP cc_start: 0.7301 (p-90) cc_final: 0.6972 (p-90) REVERT: R 217 ASN cc_start: 0.8488 (t0) cc_final: 0.8139 (t0) REVERT: R 404 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: H 5 VAL cc_start: 0.8419 (m) cc_final: 0.8214 (t) REVERT: H 11 LEU cc_start: 0.7695 (tp) cc_final: 0.7347 (mp) REVERT: H 18 ARG cc_start: 0.7191 (tpp80) cc_final: 0.6896 (tpt-90) REVERT: H 148 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8234 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7246 (mp0) cc_final: 0.6982 (mp0) REVERT: G 21 MET cc_start: 0.8355 (ttp) cc_final: 0.8068 (tpp) outliers start: 29 outliers final: 15 residues processed: 199 average time/residue: 0.0822 time to fit residues: 23.4401 Evaluate side-chains 177 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 152 VAL 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 139 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 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: 0.8980 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 287 HIS 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 = 0.3675 r_free = 0.3675 target = 0.130893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104072 restraints weight = 13668.935| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.26 r_work: 0.3109 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9077 Z= 0.146 Angle : 0.617 7.156 12354 Z= 0.318 Chirality : 0.043 0.244 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.632 83.280 1403 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.65 % Allowed : 19.36 % Favored : 76.99 % 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: -1.32 (0.24), residues: 1134 helix: 0.60 (0.26), residues: 393 sheet: -1.15 (0.32), residues: 245 loop : -1.94 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.015 0.001 TYR R 212 PHE 0.012 0.001 PHE A 339 TRP 0.021 0.001 TRP B 82 HIS 0.009 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9074) covalent geometry : angle 0.61537 (12348) SS BOND : bond 0.00590 ( 3) SS BOND : angle 1.89773 ( 6) hydrogen bonds : bond 0.03875 ( 441) hydrogen bonds : angle 4.62794 ( 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 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7717 (mm-40) REVERT: A 258 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 294 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7100 (pm20) REVERT: A 311 LYS cc_start: 0.8814 (tptp) cc_final: 0.8249 (ttpt) REVERT: A 329 THR cc_start: 0.8521 (p) cc_final: 0.8310 (t) REVERT: R 23 TRP cc_start: 0.7262 (p-90) cc_final: 0.6886 (p-90) REVERT: R 217 ASN cc_start: 0.8408 (t0) cc_final: 0.8085 (t0) REVERT: R 365 ARG cc_start: 0.7949 (ttt180) cc_final: 0.7746 (ttt180) REVERT: H 18 ARG cc_start: 0.7356 (tpp80) cc_final: 0.7054 (tpt-90) REVERT: H 148 PRO cc_start: 0.8608 (Cg_endo) cc_final: 0.8262 (Cg_exo) REVERT: H 227 TYR cc_start: 0.8329 (m-10) cc_final: 0.8057 (m-10) REVERT: G 21 MET cc_start: 0.8414 (ttp) cc_final: 0.8198 (tpp) REVERT: G 48 ASP cc_start: 0.8421 (t0) cc_final: 0.8166 (t0) outliers start: 33 outliers final: 20 residues processed: 197 average time/residue: 0.0802 time to fit residues: 22.1460 Evaluate side-chains 175 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 96 CYS 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 H residue 224 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: 5.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104784 restraints weight = 13987.079| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.29 r_work: 0.3112 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.639 9077 Z= 0.367 Angle : 0.655 24.114 12354 Z= 0.335 Chirality : 0.043 0.244 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.632 83.280 1403 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.32 % Allowed : 21.35 % Favored : 76.33 % 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: -1.32 (0.24), residues: 1134 helix: 0.60 (0.26), residues: 393 sheet: -1.15 (0.32), residues: 245 loop : -1.94 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.015 0.001 TYR R 212 PHE 0.012 0.001 PHE A 339 TRP 0.021 0.001 TRP B 82 HIS 0.009 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9074) covalent geometry : angle 0.61514 (12348) SS BOND : bond 0.36879 ( 3) SS BOND : angle 10.23158 ( 6) hydrogen bonds : bond 0.03875 ( 441) hydrogen bonds : angle 4.62794 ( 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 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7722 (mm-40) REVERT: A 258 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8682 (mt) REVERT: A 294 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7101 (pm20) REVERT: A 311 LYS cc_start: 0.8812 (tptp) cc_final: 0.8250 (ttpt) REVERT: A 329 THR cc_start: 0.8510 (p) cc_final: 0.8309 (t) REVERT: R 23 TRP cc_start: 0.7255 (p-90) cc_final: 0.6881 (p-90) REVERT: R 365 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7757 (ttt180) REVERT: H 18 ARG cc_start: 0.7364 (tpp80) cc_final: 0.7068 (tpt-90) REVERT: H 148 PRO cc_start: 0.8536 (Cg_endo) cc_final: 0.8275 (Cg_exo) REVERT: H 227 TYR cc_start: 0.8326 (m-10) cc_final: 0.8047 (m-10) REVERT: G 21 MET cc_start: 0.8380 (ttp) cc_final: 0.8166 (tpp) REVERT: G 48 ASP cc_start: 0.8412 (t0) cc_final: 0.8158 (t0) outliers start: 21 outliers final: 20 residues processed: 171 average time/residue: 0.0894 time to fit residues: 21.3333 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 96 CYS 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 H residue 224 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 111 optimal weight: 0.0030 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS R 422 ASN H 183 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 = 0.3708 r_free = 0.3708 target = 0.133350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106006 restraints weight = 13779.252| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.23 r_work: 0.3137 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9077 Z= 0.109 Angle : 0.599 9.699 12354 Z= 0.303 Chirality : 0.042 0.205 1424 Planarity : 0.004 0.059 1540 Dihedral : 7.363 88.830 1403 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.77 % Allowed : 22.01 % Favored : 75.22 % 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: -0.89 (0.24), residues: 1134 helix: 1.04 (0.26), residues: 394 sheet: -1.00 (0.32), residues: 245 loop : -1.71 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.010 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 covalent geometry : bond 0.00234 ( 9074) covalent geometry : angle 0.59686 (12348) SS BOND : bond 0.00569 ( 3) SS BOND : angle 2.27442 ( 6) hydrogen bonds : bond 0.03451 ( 441) hydrogen bonds : angle 4.45660 ( 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 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 222 ASN cc_start: 0.7963 (t0) cc_final: 0.7454 (p0) REVERT: A 258 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 294 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7134 (pm20) REVERT: R 23 TRP cc_start: 0.7204 (p-90) cc_final: 0.6870 (p-90) REVERT: R 365 ARG cc_start: 0.7778 (ttt180) cc_final: 0.7565 (ttt180) REVERT: B 127 LYS cc_start: 0.9013 (mttm) cc_final: 0.8801 (mmtt) REVERT: B 156 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8458 (pt0) REVERT: G 48 ASP cc_start: 0.8288 (t0) cc_final: 0.8079 (t0) outliers start: 25 outliers final: 16 residues processed: 188 average time/residue: 0.0841 time to fit residues: 22.3084 Evaluate side-chains 166 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3711 r_free = 0.3711 target = 0.133530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106083 restraints weight = 13657.486| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.21 r_work: 0.3143 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9077 Z= 0.116 Angle : 0.594 8.326 12354 Z= 0.302 Chirality : 0.043 0.304 1424 Planarity : 0.004 0.057 1540 Dihedral : 7.138 82.754 1402 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.99 % Allowed : 22.35 % Favored : 74.67 % 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: -0.63 (0.25), residues: 1134 helix: 1.25 (0.26), residues: 394 sheet: -0.80 (0.32), residues: 244 loop : -1.59 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 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 0.005 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9074) covalent geometry : angle 0.59313 (12348) SS BOND : bond 0.00511 ( 3) SS BOND : angle 1.84447 ( 6) hydrogen bonds : bond 0.03414 ( 441) hydrogen bonds : angle 4.38616 ( 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 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.8487 (ttp) cc_final: 0.8213 (ttm) REVERT: A 221 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 222 ASN cc_start: 0.7948 (t0) cc_final: 0.7493 (p0) REVERT: A 258 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8612 (mt) REVERT: A 294 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7138 (pm20) REVERT: A 307 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7556 (mt-10) REVERT: R 23 TRP cc_start: 0.7173 (p-90) cc_final: 0.6852 (p-90) REVERT: R 365 ARG cc_start: 0.7772 (ttt180) cc_final: 0.7535 (ttt180) REVERT: B 156 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8401 (pt0) outliers start: 27 outliers final: 20 residues processed: 186 average time/residue: 0.0864 time to fit residues: 22.4751 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 A residue 351 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 178 CYS Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS 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 156 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS H 183 GLN B 110 ASN B 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100698 restraints weight = 13975.160| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.27 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9077 Z= 0.286 Angle : 0.728 8.616 12354 Z= 0.373 Chirality : 0.049 0.274 1424 Planarity : 0.004 0.055 1540 Dihedral : 7.378 76.877 1402 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.09 % Allowed : 21.13 % Favored : 74.78 % 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: -0.89 (0.24), residues: 1134 helix: 0.97 (0.26), residues: 394 sheet: -1.06 (0.32), residues: 257 loop : -1.62 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 19 TYR 0.020 0.002 TYR B 105 PHE 0.022 0.002 PHE A 341 TRP 0.029 0.002 TRP B 82 HIS 0.009 0.002 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 9074) covalent geometry : angle 0.72544 (12348) SS BOND : bond 0.00816 ( 3) SS BOND : angle 2.86051 ( 6) hydrogen bonds : bond 0.04403 ( 441) hydrogen bonds : angle 4.60554 ( 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 199 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.291 Fit side-chains REVERT: A 222 ASN cc_start: 0.7983 (t0) cc_final: 0.7762 (p0) REVERT: A 248 MET cc_start: 0.7626 (mmm) cc_final: 0.7420 (mmm) REVERT: A 271 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8479 (tt) REVERT: A 301 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7771 (t0) REVERT: R 23 TRP cc_start: 0.7250 (p-90) cc_final: 0.6874 (p-90) REVERT: R 365 ARG cc_start: 0.7931 (ttt180) cc_final: 0.7692 (ttt180) REVERT: B 156 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8397 (pt0) outliers start: 37 outliers final: 22 residues processed: 188 average time/residue: 0.0877 time to fit residues: 23.1544 Evaluate side-chains 173 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 376 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 238 THR 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 B residue 317 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS H 183 GLN B 110 ASN B 156 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103868 restraints weight = 13795.031| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.33 r_work: 0.3088 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9077 Z= 0.159 Angle : 0.656 9.216 12354 Z= 0.335 Chirality : 0.045 0.237 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.050 64.279 1402 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 22.90 % 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: -0.73 (0.24), residues: 1134 helix: 1.15 (0.26), residues: 392 sheet: -0.96 (0.32), residues: 247 loop : -1.55 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR G 40 PHE 0.013 0.001 PHE A 341 TRP 0.022 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9074) covalent geometry : angle 0.65418 (12348) SS BOND : bond 0.00573 ( 3) SS BOND : angle 2.35490 ( 6) hydrogen bonds : bond 0.03893 ( 441) hydrogen bonds : angle 4.48510 ( 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 188 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.267 Fit side-chains REVERT: A 221 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 222 ASN cc_start: 0.7865 (t0) cc_final: 0.7425 (p0) REVERT: A 271 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 301 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7727 (t0) REVERT: R 23 TRP cc_start: 0.7250 (p-90) cc_final: 0.6875 (p-90) REVERT: R 154 PHE cc_start: 0.8208 (t80) cc_final: 0.8000 (t80) REVERT: R 365 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7604 (ttt180) REVERT: R 372 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7867 (tt) outliers start: 33 outliers final: 24 residues processed: 179 average time/residue: 0.0841 time to fit residues: 21.1723 Evaluate side-chains 173 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain B residue 65 THR 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 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: 10.0000 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3669 r_free = 0.3669 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103296 restraints weight = 13754.382| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.35 r_work: 0.3086 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9077 Z= 0.168 Angle : 0.656 9.253 12354 Z= 0.334 Chirality : 0.045 0.224 1424 Planarity : 0.004 0.058 1540 Dihedral : 6.940 58.433 1402 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.32 % Allowed : 23.23 % 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: -0.63 (0.24), residues: 1134 helix: 1.21 (0.26), residues: 392 sheet: -0.89 (0.32), residues: 247 loop : -1.50 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.010 0.001 TYR B 105 PHE 0.013 0.001 PHE A 341 TRP 0.023 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9074) covalent geometry : angle 0.65408 (12348) SS BOND : bond 0.00586 ( 3) SS BOND : angle 2.29835 ( 6) hydrogen bonds : bond 0.03859 ( 441) hydrogen bonds : angle 4.48015 ( 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 179 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.333 Fit side-chains REVERT: A 203 MET cc_start: 0.8514 (ttp) cc_final: 0.8209 (ttm) REVERT: A 221 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 222 ASN cc_start: 0.7857 (t0) cc_final: 0.7445 (p0) REVERT: A 301 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7716 (t0) REVERT: R 23 TRP cc_start: 0.7182 (p-90) cc_final: 0.6847 (p-90) REVERT: R 154 PHE cc_start: 0.8212 (t80) cc_final: 0.8004 (t80) REVERT: R 372 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7819 (tt) outliers start: 30 outliers final: 24 residues processed: 172 average time/residue: 0.0849 time to fit residues: 20.5655 Evaluate side-chains 172 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU 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 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain B residue 65 THR 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 G residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3671 r_free = 0.3671 target = 0.130352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103319 restraints weight = 13846.829| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.31 r_work: 0.3083 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9077 Z= 0.168 Angle : 0.656 9.252 12354 Z= 0.334 Chirality : 0.045 0.224 1424 Planarity : 0.004 0.058 1540 Dihedral : 6.939 58.433 1402 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.10 % Allowed : 23.67 % Favored : 73.23 % 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: -0.63 (0.24), residues: 1134 helix: 1.21 (0.26), residues: 392 sheet: -0.89 (0.32), residues: 247 loop : -1.50 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.010 0.001 TYR B 105 PHE 0.013 0.001 PHE A 341 TRP 0.023 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9074) covalent geometry : angle 0.65405 (12348) SS BOND : bond 0.00586 ( 3) SS BOND : angle 2.29827 ( 6) hydrogen bonds : bond 0.03859 ( 441) hydrogen bonds : angle 4.48015 ( 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 175 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.327 Fit side-chains REVERT: A 203 MET cc_start: 0.8513 (ttp) cc_final: 0.8215 (ttm) REVERT: A 221 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 222 ASN cc_start: 0.7846 (t0) cc_final: 0.7445 (p0) REVERT: A 301 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7649 (t0) REVERT: R 23 TRP cc_start: 0.7205 (p-90) cc_final: 0.6861 (p-90) REVERT: R 154 PHE cc_start: 0.8212 (t80) cc_final: 0.8004 (t80) REVERT: R 372 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7816 (tt) outliers start: 28 outliers final: 25 residues processed: 168 average time/residue: 0.0828 time to fit residues: 19.9430 Evaluate side-chains 172 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 404 TYR Chi-restraints excluded: chain R residue 423 LYS Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain B residue 65 THR 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 G residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 GLN B 156 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 = 0.130349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103372 restraints weight = 13650.708| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.29 r_work: 0.3087 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9077 Z= 0.168 Angle : 0.657 9.252 12354 Z= 0.334 Chirality : 0.045 0.224 1424 Planarity : 0.004 0.058 1540 Dihedral : 7.066 58.433 1402 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.10 % Allowed : 23.67 % Favored : 73.23 % 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: -0.63 (0.24), residues: 1134 helix: 1.21 (0.26), residues: 392 sheet: -0.89 (0.32), residues: 247 loop : -1.50 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.010 0.001 TYR B 105 PHE 0.013 0.001 PHE A 341 TRP 0.023 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9074) covalent geometry : angle 0.65550 (12348) SS BOND : bond 0.00586 ( 3) SS BOND : angle 2.29826 ( 6) hydrogen bonds : bond 0.03859 ( 441) hydrogen bonds : angle 4.48015 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.41 seconds wall clock time: 42 minutes 55.91 seconds (2575.91 seconds total)