Starting phenix.real_space_refine on Thu Jul 2 07:00:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2026/8dmk_27542.cif" } resolution = 3.7 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= 0.027 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 64 5.16 5 C 4601 2.51 5 N 1278 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7348 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2432 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 22, 'TRANS': 282} Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2454 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain: "G" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2391 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 16, 'TRANS': 288} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.34, per 1000 atoms: 0.18 Number of scatterers: 7348 At special positions: 0 Unit cell: (69.012, 122.472, 110.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 64 16.00 O 1404 8.00 N 1278 7.00 C 4601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 35 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 332 " distance=2.03 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 77 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 182 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 286 " - pdb=" SG CYS G 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 288 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 316 " distance=2.03 Simple disulfide: pdb=" SG CYS G 319 " - pdb=" SG CYS G 339 " 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 45 " " NAG A 402 " - " ASN A 79 " " NAG B 401 " - " ASN B 120 " " NAG G 401 " - " ASN G 60 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 292.0 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 12.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.881A pdb=" N LEU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.951A pdb=" N GLU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.794A pdb=" N THR A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.484A pdb=" N LEU B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 110 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.108A pdb=" N VAL G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 237 through 245 removed outlier: 3.721A pdb=" N THR G 245 " --> pdb=" O GLN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 264 removed outlier: 4.178A pdb=" N VAL G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 271 Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.971A pdb=" N ASN G 324 " --> pdb=" O PRO G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 4.452A pdb=" N LEU A 34 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 275 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 274 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 231 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 120 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG A 229 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N GLN A 122 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N SER A 227 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 147 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 231 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU A 145 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 233 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 143 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 235 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN A 141 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TRP A 142 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR A 158 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 144 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 190 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A 158 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.559A pdb=" N TRP A 100 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.644A pdb=" N GLN A 294 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.725A pdb=" N VAL B 262 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP B 112 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.669A pdb=" N THR B 139 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET B 265 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 137 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL B 267 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS B 135 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B 138 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 52 removed outlier: 4.167A pdb=" N SER B 51 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 124 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 149 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 238 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 147 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET B 148 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR B 165 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 150 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASP B 191 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR B 165 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 65 removed outlier: 11.634A pdb=" N LEU G 135 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N ASN G 254 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 12.939A pdb=" N LEU G 137 " --> pdb=" O THR G 252 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR G 252 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 12.403A pdb=" N LEU G 139 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 13.058A pdb=" N SER G 250 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N LYS G 141 " --> pdb=" O ASP G 248 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP G 248 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER G 159 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE G 160 " --> pdb=" O TYR G 177 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR G 177 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE G 162 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR G 175 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR G 206 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR G 177 " --> pdb=" O THR G 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 74 through 75 removed outlier: 4.380A pdb=" N GLU G 74 " --> pdb=" O CYS G 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 118 through 119 removed outlier: 3.823A pdb=" N ASP G 279 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR G 147 " --> pdb=" O GLY G 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 292 through 297 removed outlier: 5.243A pdb=" N GLU G 294 " --> pdb=" O ASN G 306 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 304 " --> pdb=" O MET G 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 311 through 312 removed outlier: 4.199A pdb=" N LYS G 318 " --> pdb=" O TYR G 312 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 237 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: 0.81 Time building geometry restraints manager: 0.73 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: 2440 1.34 - 1.46: 1818 1.46 - 1.58: 3204 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 7541 Sorted by residual: bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG G 401 " pdb=" O5 NAG G 401 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C SER G 213 " pdb=" N PRO G 214 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.60e+00 bond pdb=" CD2 HIS B 135 " pdb=" NE2 HIS B 135 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.47e+00 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 10029 1.69 - 3.38: 194 3.38 - 5.08: 18 5.08 - 6.77: 5 6.77 - 8.46: 2 Bond angle restraints: 10248 Sorted by residual: angle pdb=" CA CYS A 73 " pdb=" CB CYS A 73 " pdb=" SG CYS A 73 " ideal model delta sigma weight residual 114.40 122.86 -8.46 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CB MET B 148 " pdb=" CG MET B 148 " pdb=" SD MET B 148 " ideal model delta sigma weight residual 112.70 120.80 -8.10 3.00e+00 1.11e-01 7.29e+00 angle pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " ideal model delta sigma weight residual 114.10 109.19 4.91 2.00e+00 2.50e-01 6.04e+00 angle pdb=" N VAL G 78 " pdb=" CA VAL G 78 " pdb=" C VAL G 78 " ideal model delta sigma weight residual 108.82 106.11 2.71 1.22e+00 6.72e-01 4.93e+00 angle pdb=" CG1 ILE A 271 " pdb=" CB ILE A 271 " pdb=" CG2 ILE A 271 " ideal model delta sigma weight residual 110.70 104.30 6.40 3.00e+00 1.11e-01 4.55e+00 ... (remaining 10243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 3997 17.47 - 34.94: 406 34.94 - 52.41: 90 52.41 - 69.88: 12 69.88 - 87.35: 13 Dihedral angle restraints: 4518 sinusoidal: 1848 harmonic: 2670 Sorted by residual: dihedral pdb=" CB CYS B 65 " pdb=" SG CYS B 65 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -2.33 -83.67 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 286 " pdb=" CB CYS A 286 " ideal model delta sinusoidal sigma weight residual 93.00 166.70 -73.70 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS A 297 " pdb=" CB CYS A 297 " ideal model delta sinusoidal sigma weight residual 93.00 152.87 -59.87 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 4515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 954 0.060 - 0.121: 133 0.121 - 0.181: 10 0.181 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 1099 Sorted by residual: chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE A 271 " pdb=" CA ILE A 271 " pdb=" CG1 ILE A 271 " pdb=" CG2 ILE A 271 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL G 78 " pdb=" N VAL G 78 " pdb=" C VAL G 78 " pdb=" CB VAL G 78 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1096 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 71 " 0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO G 72 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 60 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C VAL A 60 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL A 60 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 61 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 66 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 67 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.022 5.00e-02 4.00e+02 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 1 2.12 - 2.81: 2296 2.81 - 3.51: 10254 3.51 - 4.20: 17825 4.20 - 4.90: 29420 Nonbonded interactions: 59796 Sorted by model distance: nonbonded pdb=" OD2 ASP G 108 " pdb=" OG1 THR G 116 " model vdw 1.425 3.040 nonbonded pdb=" O ARG A 69 " pdb=" OH TYR G 109 " model vdw 2.154 3.040 nonbonded pdb=" OE2 GLU A 203 " pdb=" OG SER B 200 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" OG1 THR G 80 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG A 263 " pdb=" OH TYR G 147 " model vdw 2.217 3.120 ... (remaining 59791 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.080 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 0.039 7568 Z= 0.124 Angle : 0.585 8.688 10306 Z= 0.309 Chirality : 0.044 0.301 1099 Planarity : 0.004 0.059 1342 Dihedral : 14.598 87.345 2735 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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 are not related in a simple way. whole: -1.18 (0.28), residues: 911 helix: -2.84 (0.52), residues: 59 sheet: -0.45 (0.48), residues: 135 loop : -0.69 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 262 TYR 0.019 0.001 TYR B 263 PHE 0.025 0.001 PHE A 56 TRP 0.006 0.001 TRP G 172 HIS 0.005 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7541) covalent geometry : angle 0.56987 / 0.30 (10248) SS BOND : bond 0.00245 / 0.14 ( 23) SS BOND : angle 1.42494 / 0.80 ( 46) hydrogen bonds : bond 0.30917 / 20.15 ( 104) hydrogen bonds : angle 10.51519 / 7.58 ( 237) link_NAG-ASN : bond 0.00663 / 0.37 ( 4) link_NAG-ASN : angle 2.98282 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7276 (p90) cc_final: 0.6993 (p90) REVERT: B 259 TYR cc_start: 0.7935 (p90) cc_final: 0.7723 (p90) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0583 time to fit residues: 7.1986 Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 79 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 = 0.4356 r_free = 0.4356 target = 0.117843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.097570 restraints weight = 22796.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.100727 restraints weight = 13054.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.102896 restraints weight = 8825.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.104402 restraints weight = 6669.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.105298 restraints weight = 5447.366| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7568 Z= 0.152 Angle : 0.619 10.186 10306 Z= 0.311 Chirality : 0.045 0.329 1099 Planarity : 0.005 0.056 1342 Dihedral : 4.301 22.560 1009 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.00 % Allowed : 8.48 % Favored : 90.52 % 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 are not related in a simple way. whole: -1.38 (0.27), residues: 911 helix: -2.71 (0.48), residues: 75 sheet: -0.75 (0.45), residues: 139 loop : -0.77 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 262 TYR 0.025 0.002 TYR G 175 PHE 0.017 0.001 PHE A 56 TRP 0.013 0.001 TRP G 117 HIS 0.009 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7541) covalent geometry : angle 0.60698 / 0.31 (10248) SS BOND : bond 0.00271 / 0.15 ( 23) SS BOND : angle 1.22507 / 0.74 ( 46) hydrogen bonds : bond 0.04401 / 3.02 ( 104) hydrogen bonds : angle 8.22604 / 5.74 ( 237) link_NAG-ASN : bond 0.00734 / 0.42 ( 4) link_NAG-ASN : angle 3.02147 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 HIS cc_start: 0.8074 (p-80) cc_final: 0.7545 (p90) REVERT: B 230 ILE cc_start: 0.6923 (mm) cc_final: 0.6584 (mm) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.0676 time to fit residues: 7.5776 Evaluate side-chains 77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.115633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.095314 restraints weight = 22825.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.098390 restraints weight = 13101.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.100499 restraints weight = 8931.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.101956 restraints weight = 6796.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.102841 restraints weight = 5578.300| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7568 Z= 0.160 Angle : 0.614 10.207 10306 Z= 0.308 Chirality : 0.045 0.344 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.421 22.661 1009 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.50 % Allowed : 11.35 % Favored : 87.16 % 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 are not related in a simple way. whole: -1.56 (0.27), residues: 911 helix: -2.74 (0.48), residues: 76 sheet: -1.08 (0.43), residues: 144 loop : -0.85 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.034 0.002 TYR G 175 PHE 0.011 0.001 PHE B 237 TRP 0.007 0.001 TRP B 111 HIS 0.007 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 7541) covalent geometry : angle 0.60133 / 0.30 (10248) SS BOND : bond 0.00276 / 0.16 ( 23) SS BOND : angle 1.16101 / 0.71 ( 46) hydrogen bonds : bond 0.04050 / 2.75 ( 104) hydrogen bonds : angle 7.79232 / 5.46 ( 237) link_NAG-ASN : bond 0.00763 / 0.43 ( 4) link_NAG-ASN : angle 3.15201 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7690 (p90) cc_final: 0.7352 (p90) REVERT: B 135 HIS cc_start: 0.8046 (p-80) cc_final: 0.7510 (p90) REVERT: B 230 ILE cc_start: 0.7273 (mm) cc_final: 0.6993 (mm) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.0668 time to fit residues: 7.4835 Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 HIS A 301 HIS B 225 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.114851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.094232 restraints weight = 22853.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.097357 restraints weight = 13121.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.099442 restraints weight = 8934.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.100857 restraints weight = 6808.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.101878 restraints weight = 5626.909| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7568 Z= 0.145 Angle : 0.596 10.037 10306 Z= 0.298 Chirality : 0.044 0.347 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.439 23.730 1009 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.12 % Allowed : 14.21 % Favored : 83.67 % 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 are not related in a simple way. whole: -1.58 (0.28), residues: 911 helix: -2.74 (0.48), residues: 76 sheet: -1.10 (0.45), residues: 138 loop : -0.87 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.025 0.001 TYR G 175 PHE 0.011 0.001 PHE B 237 TRP 0.007 0.001 TRP B 111 HIS 0.015 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7541) covalent geometry : angle 0.58321 / 0.29 (10248) SS BOND : bond 0.00237 / 0.13 ( 23) SS BOND : angle 1.09804 / 0.66 ( 46) hydrogen bonds : bond 0.03504 / 2.41 ( 104) hydrogen bonds : angle 7.37588 / 5.17 ( 237) link_NAG-ASN : bond 0.00742 / 0.42 ( 4) link_NAG-ASN : angle 3.21209 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7437 (p90) cc_final: 0.7142 (p90) REVERT: B 135 HIS cc_start: 0.8001 (p-80) cc_final: 0.7494 (p90) REVERT: B 230 ILE cc_start: 0.7473 (mm) cc_final: 0.7163 (mm) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.0776 time to fit residues: 9.5629 Evaluate side-chains 77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.0770 chunk 6 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 HIS A 301 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 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 = 0.4300 r_free = 0.4300 target = 0.113996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.093405 restraints weight = 22866.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.096445 restraints weight = 13217.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.098532 restraints weight = 9053.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.099970 restraints weight = 6937.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.100867 restraints weight = 5730.726| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7568 Z= 0.151 Angle : 0.606 9.593 10306 Z= 0.304 Chirality : 0.044 0.352 1099 Planarity : 0.004 0.046 1342 Dihedral : 4.526 23.850 1009 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.00 % Allowed : 16.58 % Favored : 81.42 % 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 are not related in a simple way. whole: -1.68 (0.28), residues: 911 helix: -2.91 (0.45), residues: 83 sheet: -0.97 (0.46), residues: 134 loop : -0.95 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 69 TYR 0.032 0.002 TYR G 175 PHE 0.011 0.001 PHE B 237 TRP 0.008 0.001 TRP B 111 HIS 0.009 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7541) covalent geometry : angle 0.59251 / 0.30 (10248) SS BOND : bond 0.00224 / 0.12 ( 23) SS BOND : angle 1.09756 / 0.67 ( 46) hydrogen bonds : bond 0.03457 / 2.36 ( 104) hydrogen bonds : angle 7.19207 / 5.04 ( 237) link_NAG-ASN : bond 0.00737 / 0.42 ( 4) link_NAG-ASN : angle 3.29622 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 257 ASP cc_start: 0.8834 (t0) cc_final: 0.8627 (t0) REVERT: B 135 HIS cc_start: 0.8004 (p-80) cc_final: 0.7530 (p90) REVERT: B 230 ILE cc_start: 0.7512 (mm) cc_final: 0.7212 (mm) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.0541 time to fit residues: 6.5801 Evaluate side-chains 76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 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 = 0.4303 r_free = 0.4303 target = 0.118814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.096587 restraints weight = 24193.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.099817 restraints weight = 13974.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.102050 restraints weight = 9565.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.103556 restraints weight = 7304.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.104480 restraints weight = 6027.320| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7568 Z= 0.130 Angle : 0.602 9.322 10306 Z= 0.302 Chirality : 0.045 0.348 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.458 24.347 1009 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.75 % Allowed : 18.70 % Favored : 79.55 % 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 are not related in a simple way. whole: -1.70 (0.28), residues: 911 helix: -3.19 (0.42), residues: 81 sheet: -0.90 (0.47), residues: 134 loop : -0.96 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.023 0.001 TYR G 175 PHE 0.011 0.001 PHE B 237 TRP 0.009 0.001 TRP B 111 HIS 0.007 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7541) covalent geometry : angle 0.58907 / 0.30 (10248) SS BOND : bond 0.00187 / 0.11 ( 23) SS BOND : angle 1.08210 / 0.66 ( 46) hydrogen bonds : bond 0.03396 / 2.36 ( 104) hydrogen bonds : angle 6.92970 / 4.85 ( 237) link_NAG-ASN : bond 0.00691 / 0.39 ( 4) link_NAG-ASN : angle 3.23549 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 246 MET cc_start: 0.5866 (tmm) cc_final: 0.5646 (tmm) REVERT: B 163 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: B 230 ILE cc_start: 0.7597 (mm) cc_final: 0.7297 (mm) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.0669 time to fit residues: 7.6623 Evaluate side-chains 74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 112 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 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 = 0.4285 r_free = 0.4285 target = 0.114827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.093417 restraints weight = 23666.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.096487 restraints weight = 13809.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.098585 restraints weight = 9529.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.100034 restraints weight = 7348.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.101040 restraints weight = 6116.971| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7568 Z= 0.161 Angle : 0.627 9.492 10306 Z= 0.315 Chirality : 0.045 0.356 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.600 24.692 1009 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.24 % Allowed : 19.08 % Favored : 78.68 % 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 are not related in a simple way. whole: -1.74 (0.28), residues: 911 helix: -2.62 (0.46), residues: 80 sheet: -0.93 (0.47), residues: 131 loop : -1.07 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.030 0.002 TYR G 175 PHE 0.009 0.001 PHE B 237 TRP 0.009 0.001 TRP A 113 HIS 0.007 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 7541) covalent geometry : angle 0.61189 / 0.31 (10248) SS BOND : bond 0.00236 / 0.13 ( 23) SS BOND : angle 1.31704 / 0.77 ( 46) hydrogen bonds : bond 0.03563 / 2.45 ( 104) hydrogen bonds : angle 7.03218 / 4.91 ( 237) link_NAG-ASN : bond 0.00771 / 0.44 ( 4) link_NAG-ASN : angle 3.42443 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.268 Fit side-chains REVERT: B 163 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: B 230 ILE cc_start: 0.7607 (mm) cc_final: 0.7324 (mm) outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 0.0603 time to fit residues: 7.0796 Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 318 GLN B 90 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.108680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.088040 restraints weight = 23463.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.090985 restraints weight = 13533.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.092964 restraints weight = 9288.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.094307 restraints weight = 7163.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.095120 restraints weight = 5988.203| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7568 Z= 0.280 Angle : 0.756 9.906 10306 Z= 0.386 Chirality : 0.048 0.377 1099 Planarity : 0.005 0.049 1342 Dihedral : 5.205 28.692 1009 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 1.87 % Allowed : 21.20 % Favored : 76.93 % 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 are not related in a simple way. whole: -2.04 (0.27), residues: 911 helix: -2.77 (0.49), residues: 66 sheet: -1.19 (0.48), residues: 131 loop : -1.34 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 234 TYR 0.041 0.002 TYR G 175 PHE 0.012 0.002 PHE A 153 TRP 0.016 0.002 TRP A 113 HIS 0.012 0.002 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 ( 7541) covalent geometry : angle 0.73889 / 0.38 (10248) SS BOND : bond 0.00403 / 0.22 ( 23) SS BOND : angle 1.49803 / 0.91 ( 46) hydrogen bonds : bond 0.04455 / 3.02 ( 104) hydrogen bonds : angle 7.48023 / 5.25 ( 237) link_NAG-ASN : bond 0.01057 / 0.63 ( 4) link_NAG-ASN : angle 3.96415 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.289 Fit side-chains REVERT: B 230 ILE cc_start: 0.7614 (mm) cc_final: 0.7253 (mm) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.0614 time to fit residues: 6.3930 Evaluate side-chains 66 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** 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 = 0.4248 r_free = 0.4248 target = 0.112064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.090773 restraints weight = 22658.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.093804 restraints weight = 12931.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.095864 restraints weight = 8874.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.097268 restraints weight = 6829.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.098109 restraints weight = 5696.946| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7568 Z= 0.191 Angle : 0.685 10.059 10306 Z= 0.344 Chirality : 0.046 0.358 1099 Planarity : 0.005 0.046 1342 Dihedral : 5.063 26.421 1009 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.50 % Allowed : 21.45 % Favored : 77.06 % 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 are not related in a simple way. whole: -2.01 (0.27), residues: 911 helix: -2.65 (0.49), residues: 66 sheet: -1.20 (0.48), residues: 131 loop : -1.31 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.027 0.002 TYR G 175 PHE 0.011 0.002 PHE G 222 TRP 0.013 0.001 TRP A 113 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 7541) covalent geometry : angle 0.66874 / 0.34 (10248) SS BOND : bond 0.00267 / 0.15 ( 23) SS BOND : angle 1.39649 / 0.83 ( 46) hydrogen bonds : bond 0.03772 / 2.56 ( 104) hydrogen bonds : angle 7.14890 / 5.01 ( 237) link_NAG-ASN : bond 0.00794 / 0.46 ( 4) link_NAG-ASN : angle 3.69870 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.281 Fit side-chains REVERT: B 116 ASN cc_start: 0.8321 (p0) cc_final: 0.8099 (m-40) REVERT: B 163 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: B 230 ILE cc_start: 0.7579 (mm) cc_final: 0.7266 (mm) REVERT: G 175 TYR cc_start: 0.6318 (m-80) cc_final: 0.6090 (m-80) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.0574 time to fit residues: 5.8749 Evaluate side-chains 66 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN A 112 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.115288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.094272 restraints weight = 22574.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.097406 restraints weight = 12905.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.099496 restraints weight = 8825.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.100986 restraints weight = 6770.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.101974 restraints weight = 5596.519| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7568 Z= 0.120 Angle : 0.655 10.999 10306 Z= 0.323 Chirality : 0.046 0.345 1099 Planarity : 0.004 0.044 1342 Dihedral : 4.799 24.679 1009 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.25 % Allowed : 21.95 % Favored : 76.81 % 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 are not related in a simple way. whole: -1.92 (0.27), residues: 911 helix: -3.15 (0.44), residues: 75 sheet: -1.11 (0.47), residues: 136 loop : -1.16 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.024 0.001 TYR G 175 PHE 0.012 0.001 PHE G 222 TRP 0.013 0.001 TRP A 100 HIS 0.011 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 7541) covalent geometry : angle 0.64063 / 0.32 (10248) SS BOND : bond 0.00173 / 0.11 ( 23) SS BOND : angle 1.33134 / 0.78 ( 46) hydrogen bonds : bond 0.03257 / 2.25 ( 104) hydrogen bonds : angle 6.79744 / 4.74 ( 237) link_NAG-ASN : bond 0.00677 / 0.38 ( 4) link_NAG-ASN : angle 3.34548 / 1.51 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.208 Fit side-chains REVERT: B 230 ILE cc_start: 0.7575 (mm) cc_final: 0.7176 (mm) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.0603 time to fit residues: 6.4883 Evaluate side-chains 65 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 4 optimal weight: 0.8980 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 HIS A 301 HIS B 225 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.114654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.094537 restraints weight = 22508.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.097672 restraints weight = 12814.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.099771 restraints weight = 8678.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.101232 restraints weight = 6597.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.102123 restraints weight = 5409.583| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7568 Z= 0.116 Angle : 0.654 10.628 10306 Z= 0.322 Chirality : 0.045 0.347 1099 Planarity : 0.004 0.044 1342 Dihedral : 4.682 24.139 1009 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.12 % Allowed : 22.57 % Favored : 76.31 % 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 are not related in a simple way. whole: -1.66 (0.27), residues: 911 helix: -2.72 (0.53), residues: 61 sheet: -0.69 (0.49), residues: 122 loop : -1.11 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 152 TYR 0.040 0.002 TYR G 175 PHE 0.021 0.001 PHE G 222 TRP 0.015 0.001 TRP A 100 HIS 0.011 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7541) covalent geometry : angle 0.64086 / 0.32 (10248) SS BOND : bond 0.00166 / 0.11 ( 23) SS BOND : angle 1.29435 / 0.79 ( 46) hydrogen bonds : bond 0.03077 / 2.14 ( 104) hydrogen bonds : angle 6.55722 / 4.56 ( 237) link_NAG-ASN : bond 0.00678 / 0.38 ( 4) link_NAG-ASN : angle 3.25037 / 1.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.26 seconds wall clock time: 20 minutes 32.37 seconds (1232.37 seconds total)