Starting phenix.real_space_refine on Sat Aug 23 02:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jso_36625/08_2025/8jso_36625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jso_36625/08_2025/8jso_36625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jso_36625/08_2025/8jso_36625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jso_36625/08_2025/8jso_36625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jso_36625/08_2025/8jso_36625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jso_36625/08_2025/8jso_36625.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5764 2.51 5 N 1546 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9045 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2292 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.18 Number of scatterers: 9045 At special positions: 0 Unit cell: (113.9, 130.05, 111.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1667 8.00 N 1546 7.00 C 5764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 335.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE R 401 " Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.6% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.046A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.649A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.113A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.883A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.616A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.557A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.664A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 51 removed outlier: 3.706A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.576A pdb=" N GLU R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 123 removed outlier: 4.403A pdb=" N PHE R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS R 96 " --> pdb=" O GLY R 92 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 removed outlier: 3.860A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix removed outlier: 4.256A pdb=" N MET R 158 " --> pdb=" O PHE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 178 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 200 through 228 removed outlier: 4.116A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.058A pdb=" N VAL R 259 " --> pdb=" O ILE R 255 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.963A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.614A pdb=" N ALA R 305 " --> pdb=" O PRO R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.926A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.871A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.657A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 191 removed outlier: 7.332A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.385A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.153A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.594A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.963A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.589A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN S 82 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.510A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.580A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.961A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 4.022A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1164 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: 1.13 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2899 1.34 - 1.46: 2070 1.46 - 1.58: 4177 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 9248 Sorted by residual: bond pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.22e+00 bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.57e-02 4.06e+03 5.25e+00 bond pdb=" CA VAL R 150 " pdb=" CB VAL R 150 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 3.95e+00 bond pdb=" N SER B 331 " pdb=" CA SER B 331 " ideal model delta sigma weight residual 1.455 1.479 -0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CG MET Y 38 " pdb=" SD MET Y 38 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 12028 1.52 - 3.04: 400 3.04 - 4.56: 71 4.56 - 6.09: 15 6.09 - 7.61: 6 Bond angle restraints: 12520 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.24 4.23 1.01e+00 9.80e-01 1.75e+01 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 112.96 109.01 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA MET Y 38 " pdb=" CB MET Y 38 " pdb=" CG MET Y 38 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C LEU Y 37 " pdb=" N MET Y 38 " pdb=" CA MET Y 38 " ideal model delta sigma weight residual 121.14 115.75 5.39 1.75e+00 3.27e-01 9.48e+00 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 112.92 109.20 3.72 1.23e+00 6.61e-01 9.15e+00 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4938 17.91 - 35.82: 440 35.82 - 53.72: 87 53.72 - 71.63: 12 71.63 - 89.54: 6 Dihedral angle restraints: 5483 sinusoidal: 2152 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual -86.00 -113.68 27.68 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ILE R 201 " pdb=" C ILE R 201 " pdb=" N PRO R 202 " pdb=" CA PRO R 202 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual -180.00 -135.81 -44.19 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1084 0.047 - 0.094: 250 0.094 - 0.140: 60 0.140 - 0.187: 1 0.187 - 0.234: 2 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB ILE R 201 " pdb=" CA ILE R 201 " pdb=" CG1 ILE R 201 " pdb=" CG2 ILE R 201 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR A 292 " pdb=" CA THR A 292 " pdb=" OG1 THR A 292 " pdb=" CG2 THR A 292 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" C PRO A 299 " pdb=" CB PRO A 299 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1394 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 201 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO R 202 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 281 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO R 282 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 282 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 282 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO S 151 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.023 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1323 2.76 - 3.29: 8742 3.29 - 3.83: 14254 3.83 - 4.36: 16207 4.36 - 4.90: 28857 Nonbonded interactions: 69383 Sorted by model distance: nonbonded pdb=" NE2 GLN A 52 " pdb=" OD1 ASP A 335 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.227 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.278 3.040 ... (remaining 69378 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9251 Z= 0.161 Angle : 0.668 7.608 12526 Z= 0.374 Chirality : 0.042 0.234 1397 Planarity : 0.004 0.079 1584 Dihedral : 13.944 89.539 3326 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.64 (0.25), residues: 1129 helix: 1.54 (0.27), residues: 393 sheet: -0.72 (0.33), residues: 243 loop : -1.94 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.009 0.001 TYR S 173 PHE 0.024 0.001 PHE A 307 TRP 0.015 0.001 TRP R 148 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9248) covalent geometry : angle 0.66753 (12520) SS BOND : bond 0.00380 ( 3) SS BOND : angle 0.83426 ( 6) hydrogen bonds : bond 0.19090 ( 403) hydrogen bonds : angle 6.77514 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.231 Fit side-chains REVERT: A 307 PHE cc_start: 0.8004 (t80) cc_final: 0.7803 (t80) REVERT: B 17 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9056 (tm-30) REVERT: B 295 ASN cc_start: 0.8143 (m-40) cc_final: 0.7904 (m-40) REVERT: B 308 LEU cc_start: 0.8041 (mp) cc_final: 0.7781 (mp) REVERT: R 31 VAL cc_start: 0.8535 (p) cc_final: 0.8286 (p) REVERT: R 222 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6744 (tmm160) REVERT: S 11 LEU cc_start: 0.6560 (pt) cc_final: 0.5728 (tt) REVERT: S 95 TYR cc_start: 0.6714 (m-10) cc_final: 0.6118 (m-10) REVERT: S 227 TYR cc_start: 0.6983 (m-80) cc_final: 0.6499 (m-80) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0783 time to fit residues: 19.6123 Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.197557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125221 restraints weight = 11850.032| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.65 r_work: 0.3300 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9251 Z= 0.293 Angle : 0.734 11.507 12526 Z= 0.384 Chirality : 0.048 0.201 1397 Planarity : 0.005 0.069 1584 Dihedral : 5.117 50.564 1252 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.93 % Allowed : 10.65 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.92 (0.25), residues: 1129 helix: 1.31 (0.26), residues: 395 sheet: -0.89 (0.32), residues: 255 loop : -2.15 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.023 0.002 TYR R 172 PHE 0.021 0.002 PHE R 311 TRP 0.021 0.002 TRP R 148 HIS 0.009 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 9248) covalent geometry : angle 0.73383 (12520) SS BOND : bond 0.00724 ( 3) SS BOND : angle 1.36011 ( 6) hydrogen bonds : bond 0.06887 ( 403) hydrogen bonds : angle 5.43629 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8691 (pttp) REVERT: B 217 MET cc_start: 0.8451 (ptm) cc_final: 0.8151 (ppp) REVERT: B 295 ASN cc_start: 0.8557 (m-40) cc_final: 0.8034 (m-40) REVERT: R 143 MET cc_start: 0.7936 (mtt) cc_final: 0.7539 (mtt) REVERT: S 95 TYR cc_start: 0.6936 (m-10) cc_final: 0.6347 (m-10) REVERT: S 174 LEU cc_start: 0.6676 (tp) cc_final: 0.6142 (mp) REVERT: S 228 TYR cc_start: 0.6614 (m-80) cc_final: 0.6401 (m-80) REVERT: Y 44 HIS cc_start: 0.8348 (m90) cc_final: 0.7733 (m-70) outliers start: 19 outliers final: 13 residues processed: 169 average time/residue: 0.0778 time to fit residues: 18.7337 Evaluate side-chains 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN R 300 ASN ** S 231 GLN ** 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 = 0.4390 r_free = 0.4390 target = 0.203715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131928 restraints weight = 11776.605| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.05 r_work: 0.3454 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9251 Z= 0.121 Angle : 0.579 10.889 12526 Z= 0.296 Chirality : 0.042 0.157 1397 Planarity : 0.004 0.048 1584 Dihedral : 4.699 50.068 1252 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.62 % Allowed : 12.78 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.48 (0.26), residues: 1129 helix: 1.84 (0.27), residues: 395 sheet: -0.78 (0.31), residues: 268 loop : -1.99 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.019 0.001 TYR R 27 PHE 0.016 0.001 PHE R 91 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9248) covalent geometry : angle 0.57850 (12520) SS BOND : bond 0.00465 ( 3) SS BOND : angle 0.62566 ( 6) hydrogen bonds : bond 0.04662 ( 403) hydrogen bonds : angle 4.73798 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 186 GLU cc_start: 0.7429 (tt0) cc_final: 0.7182 (tm-30) REVERT: B 10 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: B 246 ASP cc_start: 0.8294 (m-30) cc_final: 0.8075 (m-30) REVERT: B 253 PHE cc_start: 0.8244 (m-10) cc_final: 0.7967 (m-10) REVERT: B 256 ARG cc_start: 0.8994 (tpp80) cc_final: 0.8493 (tpt170) REVERT: B 295 ASN cc_start: 0.8467 (m-40) cc_final: 0.8134 (m-40) REVERT: R 81 MET cc_start: 0.8557 (ttp) cc_final: 0.8233 (ttm) REVERT: R 143 MET cc_start: 0.7995 (mtt) cc_final: 0.7725 (mtt) REVERT: R 222 ARG cc_start: 0.7447 (ttp80) cc_final: 0.6993 (tmm160) REVERT: R 317 MET cc_start: 0.7800 (tmm) cc_final: 0.7574 (tmm) REVERT: S 95 TYR cc_start: 0.6905 (m-10) cc_final: 0.6469 (m-10) REVERT: S 174 LEU cc_start: 0.6662 (tp) cc_final: 0.6232 (mp) REVERT: Y 28 ILE cc_start: 0.8710 (pt) cc_final: 0.8372 (pt) REVERT: Y 44 HIS cc_start: 0.8256 (m90) cc_final: 0.7389 (m170) outliers start: 16 outliers final: 9 residues processed: 175 average time/residue: 0.0762 time to fit residues: 18.8187 Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN R 63 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.203730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131952 restraints weight = 11919.059| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.08 r_work: 0.3455 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9251 Z= 0.119 Angle : 0.570 10.908 12526 Z= 0.291 Chirality : 0.042 0.157 1397 Planarity : 0.004 0.043 1584 Dihedral : 4.612 49.677 1252 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.83 % Allowed : 14.60 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.36 (0.26), residues: 1129 helix: 1.93 (0.27), residues: 395 sheet: -0.77 (0.31), residues: 272 loop : -1.88 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 222 TYR 0.013 0.001 TYR R 172 PHE 0.017 0.001 PHE R 91 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9248) covalent geometry : angle 0.56991 (12520) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.76349 ( 6) hydrogen bonds : bond 0.04403 ( 403) hydrogen bonds : angle 4.54599 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.248 Fit side-chains REVERT: A 38 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 186 GLU cc_start: 0.7383 (tt0) cc_final: 0.7134 (tm-30) REVERT: B 10 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: B 246 ASP cc_start: 0.8366 (m-30) cc_final: 0.8162 (m-30) REVERT: B 253 PHE cc_start: 0.8302 (m-10) cc_final: 0.7979 (m-10) REVERT: B 256 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8488 (tpt170) REVERT: B 295 ASN cc_start: 0.8500 (m-40) cc_final: 0.7942 (m-40) REVERT: R 81 MET cc_start: 0.8538 (ttp) cc_final: 0.8215 (ttm) REVERT: R 222 ARG cc_start: 0.7447 (ttp80) cc_final: 0.6989 (tmm160) REVERT: R 317 MET cc_start: 0.7786 (tmm) cc_final: 0.7550 (tmm) REVERT: S 51 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.5799 (mp) REVERT: S 95 TYR cc_start: 0.6726 (m-10) cc_final: 0.6384 (m-10) REVERT: S 174 LEU cc_start: 0.6774 (tp) cc_final: 0.6393 (mp) REVERT: S 230 MET cc_start: 0.2956 (mmm) cc_final: 0.2751 (mmm) REVERT: Y 28 ILE cc_start: 0.8689 (pt) cc_final: 0.8401 (pt) REVERT: Y 38 MET cc_start: 0.8416 (pmm) cc_final: 0.8043 (pmm) REVERT: Y 44 HIS cc_start: 0.8194 (m90) cc_final: 0.7317 (m170) outliers start: 18 outliers final: 11 residues processed: 171 average time/residue: 0.0765 time to fit residues: 18.5074 Evaluate side-chains 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** S 231 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 = 0.4385 r_free = 0.4385 target = 0.203013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131053 restraints weight = 11893.418| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.06 r_work: 0.3446 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9251 Z= 0.134 Angle : 0.595 10.917 12526 Z= 0.300 Chirality : 0.042 0.159 1397 Planarity : 0.004 0.047 1584 Dihedral : 4.585 50.040 1252 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.04 % Allowed : 15.21 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.33 (0.26), residues: 1129 helix: 1.88 (0.27), residues: 397 sheet: -0.71 (0.32), residues: 272 loop : -1.83 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.020 0.001 TYR R 27 PHE 0.017 0.001 PHE R 91 TRP 0.022 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9248) covalent geometry : angle 0.59481 (12520) SS BOND : bond 0.00538 ( 3) SS BOND : angle 0.60267 ( 6) hydrogen bonds : bond 0.04534 ( 403) hydrogen bonds : angle 4.50785 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 186 GLU cc_start: 0.7370 (tt0) cc_final: 0.7106 (tm-30) REVERT: B 10 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: B 246 ASP cc_start: 0.8398 (m-30) cc_final: 0.8190 (m-30) REVERT: B 254 ASP cc_start: 0.8695 (t0) cc_final: 0.7543 (p0) REVERT: B 256 ARG cc_start: 0.9001 (tpp80) cc_final: 0.8425 (tpt170) REVERT: B 295 ASN cc_start: 0.8470 (m-40) cc_final: 0.8046 (m-40) REVERT: R 81 MET cc_start: 0.8537 (ttp) cc_final: 0.8175 (ttm) REVERT: R 143 MET cc_start: 0.8037 (mtt) cc_final: 0.7770 (mtt) REVERT: R 222 ARG cc_start: 0.7438 (ttp80) cc_final: 0.6988 (tmm160) REVERT: S 51 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5806 (mp) REVERT: S 95 TYR cc_start: 0.6736 (m-10) cc_final: 0.6332 (m-10) REVERT: S 174 LEU cc_start: 0.6680 (tp) cc_final: 0.6352 (mp) REVERT: Y 38 MET cc_start: 0.8314 (pmm) cc_final: 0.7949 (pmm) REVERT: Y 44 HIS cc_start: 0.8287 (m90) cc_final: 0.7385 (m170) outliers start: 30 outliers final: 19 residues processed: 176 average time/residue: 0.0822 time to fit residues: 20.4614 Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.202953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131091 restraints weight = 11931.665| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.09 r_work: 0.3452 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9251 Z= 0.132 Angle : 0.599 10.832 12526 Z= 0.300 Chirality : 0.042 0.158 1397 Planarity : 0.004 0.048 1584 Dihedral : 4.570 50.503 1252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.64 % Allowed : 16.02 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.29 (0.26), residues: 1129 helix: 1.94 (0.27), residues: 395 sheet: -0.72 (0.31), residues: 278 loop : -1.79 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.014 0.001 TYR S 103 PHE 0.018 0.001 PHE R 91 TRP 0.026 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9248) covalent geometry : angle 0.59952 (12520) SS BOND : bond 0.00500 ( 3) SS BOND : angle 0.54306 ( 6) hydrogen bonds : bond 0.04460 ( 403) hydrogen bonds : angle 4.40749 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.315 Fit side-chains REVERT: A 38 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8727 (tt) REVERT: A 186 GLU cc_start: 0.7371 (tt0) cc_final: 0.7098 (tm-30) REVERT: B 10 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 121 CYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6819 (m) REVERT: B 175 GLN cc_start: 0.8052 (pm20) cc_final: 0.7475 (pm20) REVERT: B 214 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7779 (mmm-85) REVERT: B 246 ASP cc_start: 0.8402 (m-30) cc_final: 0.8184 (m-30) REVERT: B 256 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8568 (tpt170) REVERT: B 295 ASN cc_start: 0.8515 (m-40) cc_final: 0.8071 (m-40) REVERT: R 81 MET cc_start: 0.8540 (ttp) cc_final: 0.8198 (ttm) REVERT: R 222 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7011 (tmm160) REVERT: S 51 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5813 (mp) REVERT: S 95 TYR cc_start: 0.6741 (m-10) cc_final: 0.6384 (m-10) REVERT: S 174 LEU cc_start: 0.6766 (tp) cc_final: 0.6461 (mp) REVERT: S 233 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.3776 (mm) REVERT: Y 44 HIS cc_start: 0.8266 (m90) cc_final: 0.7385 (m170) outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.0800 time to fit residues: 20.6397 Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 0.0770 chunk 83 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 0.0060 chunk 110 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.208263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138081 restraints weight = 11905.379| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.06 r_work: 0.3530 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9251 Z= 0.107 Angle : 0.586 11.138 12526 Z= 0.293 Chirality : 0.041 0.178 1397 Planarity : 0.004 0.048 1584 Dihedral : 4.394 51.429 1252 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.03 % Allowed : 17.55 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.10 (0.26), residues: 1129 helix: 2.06 (0.27), residues: 397 sheet: -0.63 (0.31), residues: 289 loop : -1.68 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.021 0.001 TYR R 27 PHE 0.015 0.001 PHE A 189 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9248) covalent geometry : angle 0.58570 (12520) SS BOND : bond 0.00387 ( 3) SS BOND : angle 0.29222 ( 6) hydrogen bonds : bond 0.03515 ( 403) hydrogen bonds : angle 4.14220 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7571 (t0) cc_final: 0.6883 (t0) REVERT: B 10 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: B 175 GLN cc_start: 0.7982 (pm20) cc_final: 0.7409 (pm20) REVERT: B 246 ASP cc_start: 0.8360 (m-30) cc_final: 0.8150 (m-30) REVERT: B 253 PHE cc_start: 0.8398 (m-10) cc_final: 0.8118 (m-10) REVERT: B 254 ASP cc_start: 0.8801 (t0) cc_final: 0.7746 (p0) REVERT: B 256 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8415 (tpt170) REVERT: B 295 ASN cc_start: 0.8547 (m-40) cc_final: 0.8115 (m-40) REVERT: R 89 TRP cc_start: 0.7145 (t-100) cc_final: 0.6819 (t-100) REVERT: R 222 ARG cc_start: 0.7366 (ttp80) cc_final: 0.6930 (tmm160) REVERT: S 95 TYR cc_start: 0.6747 (m-10) cc_final: 0.6492 (m-10) REVERT: S 174 LEU cc_start: 0.6820 (tp) cc_final: 0.6518 (mp) REVERT: Y 44 HIS cc_start: 0.8033 (m90) cc_final: 0.7096 (m170) outliers start: 20 outliers final: 13 residues processed: 183 average time/residue: 0.0755 time to fit residues: 19.7241 Evaluate side-chains 170 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain Y residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.205015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133120 restraints weight = 11970.505| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.10 r_work: 0.3465 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9251 Z= 0.125 Angle : 0.609 10.973 12526 Z= 0.306 Chirality : 0.042 0.158 1397 Planarity : 0.004 0.049 1584 Dihedral : 4.443 51.974 1252 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.13 % Allowed : 18.05 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.07 (0.26), residues: 1129 helix: 1.98 (0.27), residues: 400 sheet: -0.57 (0.32), residues: 280 loop : -1.59 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.024 0.001 TYR S 103 PHE 0.017 0.001 PHE R 91 TRP 0.023 0.001 TRP B 339 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9248) covalent geometry : angle 0.60895 (12520) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.89555 ( 6) hydrogen bonds : bond 0.04107 ( 403) hydrogen bonds : angle 4.21718 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.247 Fit side-chains REVERT: B 10 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 121 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6867 (m) REVERT: B 175 GLN cc_start: 0.8042 (pm20) cc_final: 0.7437 (pm20) REVERT: B 214 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7751 (mmm-85) REVERT: B 246 ASP cc_start: 0.8411 (m-30) cc_final: 0.8201 (m-30) REVERT: B 256 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8563 (tpt170) REVERT: B 295 ASN cc_start: 0.8581 (m-40) cc_final: 0.8121 (m-40) REVERT: R 81 MET cc_start: 0.8704 (ttp) cc_final: 0.8331 (ttm) REVERT: R 89 TRP cc_start: 0.7178 (t-100) cc_final: 0.6802 (t-100) REVERT: R 222 ARG cc_start: 0.7388 (ttp80) cc_final: 0.6955 (tmm160) REVERT: S 95 TYR cc_start: 0.6665 (m-10) cc_final: 0.6262 (m-10) REVERT: S 188 LEU cc_start: 0.7401 (mp) cc_final: 0.6580 (tp) REVERT: Y 44 HIS cc_start: 0.8059 (m90) cc_final: 0.7121 (m170) outliers start: 21 outliers final: 14 residues processed: 168 average time/residue: 0.0825 time to fit residues: 19.3043 Evaluate side-chains 170 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.202484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132937 restraints weight = 11943.137| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.62 r_work: 0.3358 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9251 Z= 0.161 Angle : 0.656 10.696 12526 Z= 0.329 Chirality : 0.043 0.167 1397 Planarity : 0.004 0.051 1584 Dihedral : 4.585 51.368 1252 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.33 % Allowed : 18.15 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.24 (0.26), residues: 1129 helix: 1.80 (0.26), residues: 399 sheet: -0.66 (0.32), residues: 275 loop : -1.63 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.022 0.001 TYR S 103 PHE 0.018 0.001 PHE R 91 TRP 0.025 0.002 TRP B 339 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9248) covalent geometry : angle 0.65619 (12520) SS BOND : bond 0.00433 ( 3) SS BOND : angle 0.79727 ( 6) hydrogen bonds : bond 0.04811 ( 403) hydrogen bonds : angle 4.40323 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.269 Fit side-chains REVERT: B 10 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: B 17 GLN cc_start: 0.9002 (pp30) cc_final: 0.8558 (pp30) REVERT: B 121 CYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6771 (m) REVERT: B 214 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7851 (mmm-85) REVERT: B 246 ASP cc_start: 0.8468 (m-30) cc_final: 0.8247 (m-30) REVERT: B 254 ASP cc_start: 0.8866 (t0) cc_final: 0.7703 (p0) REVERT: B 256 ARG cc_start: 0.8915 (tpp80) cc_final: 0.8450 (tpt170) REVERT: B 295 ASN cc_start: 0.8613 (m-40) cc_final: 0.8190 (m-40) REVERT: R 65 MET cc_start: 0.7639 (ttt) cc_final: 0.7433 (ttp) REVERT: R 222 ARG cc_start: 0.7350 (ttp80) cc_final: 0.6923 (tmm160) REVERT: S 95 TYR cc_start: 0.6790 (m-10) cc_final: 0.6337 (m-10) REVERT: S 174 LEU cc_start: 0.6707 (mt) cc_final: 0.6252 (mp) REVERT: S 219 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6255 (tt) REVERT: Y 44 HIS cc_start: 0.8156 (m90) cc_final: 0.7227 (m170) outliers start: 23 outliers final: 16 residues processed: 173 average time/residue: 0.0767 time to fit residues: 18.8079 Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 225 HIS R 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.197938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125253 restraints weight = 11860.641| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.40 r_work: 0.3341 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9251 Z= 0.246 Angle : 0.733 10.925 12526 Z= 0.374 Chirality : 0.046 0.213 1397 Planarity : 0.005 0.053 1584 Dihedral : 4.933 50.096 1252 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.23 % Allowed : 17.75 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.57 (0.25), residues: 1129 helix: 1.53 (0.26), residues: 395 sheet: -0.73 (0.32), residues: 273 loop : -1.88 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.023 0.002 TYR S 103 PHE 0.022 0.002 PHE R 91 TRP 0.030 0.002 TRP B 339 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 9248) covalent geometry : angle 0.73237 (12520) SS BOND : bond 0.00583 ( 3) SS BOND : angle 1.16495 ( 6) hydrogen bonds : bond 0.06161 ( 403) hydrogen bonds : angle 4.80257 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.271 Fit side-chains REVERT: A 53 MET cc_start: 0.8144 (mmm) cc_final: 0.7605 (mmm) REVERT: B 10 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: B 17 GLN cc_start: 0.9015 (pp30) cc_final: 0.8577 (pp30) REVERT: B 121 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7034 (m) REVERT: B 214 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7796 (mmm-85) REVERT: B 256 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8521 (tpt170) REVERT: B 259 GLN cc_start: 0.8584 (tp40) cc_final: 0.8276 (tp40) REVERT: B 295 ASN cc_start: 0.8550 (m-40) cc_final: 0.8156 (m-40) REVERT: R 81 MET cc_start: 0.8706 (ttp) cc_final: 0.8336 (ttm) REVERT: S 29 PHE cc_start: 0.7853 (t80) cc_final: 0.7189 (t80) REVERT: S 51 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.5889 (mp) REVERT: S 174 LEU cc_start: 0.6617 (mt) cc_final: 0.6241 (mp) REVERT: S 188 LEU cc_start: 0.7436 (mp) cc_final: 0.6622 (tp) REVERT: S 219 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6296 (tt) REVERT: Y 44 HIS cc_start: 0.8332 (m90) cc_final: 0.7758 (m-70) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 0.0801 time to fit residues: 20.5446 Evaluate side-chains 178 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 225 HIS R 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.201764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129708 restraints weight = 11770.868| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.06 r_work: 0.3426 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9251 Z= 0.150 Angle : 0.680 11.111 12526 Z= 0.341 Chirality : 0.044 0.218 1397 Planarity : 0.004 0.052 1584 Dihedral : 4.739 49.176 1252 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.03 % Allowed : 18.05 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.39 (0.26), residues: 1129 helix: 1.74 (0.27), residues: 396 sheet: -0.71 (0.32), residues: 278 loop : -1.80 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.022 0.001 TYR S 103 PHE 0.020 0.001 PHE R 91 TRP 0.023 0.002 TRP B 339 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9248) covalent geometry : angle 0.67951 (12520) SS BOND : bond 0.00449 ( 3) SS BOND : angle 0.72100 ( 6) hydrogen bonds : bond 0.04866 ( 403) hydrogen bonds : angle 4.55638 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.13 seconds wall clock time: 41 minutes 19.13 seconds (2479.13 seconds total)