Starting phenix.real_space_refine on Wed Feb 4 06:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vif_65089/02_2026/9vif_65089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vif_65089/02_2026/9vif_65089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vif_65089/02_2026/9vif_65089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vif_65089/02_2026/9vif_65089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vif_65089/02_2026/9vif_65089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vif_65089/02_2026/9vif_65089.map" } resolution = 3.19 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= 0.017 sd= 0.999 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 5757 2.51 5 N 1548 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2398 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1754 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "C" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 9038 At special positions: 0 Unit cell: (94.08, 122.88, 138.24, 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 1665 8.00 N 1548 7.00 C 5757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 203 " distance=2.05 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: 0.53 Conformation dependent library (CDL) restraints added in 221.8 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 37.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 39 through 71 removed outlier: 3.625A pdb=" N ASN A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.757A pdb=" N HIS A 75 " --> pdb=" O ARG A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 76 through 104 removed outlier: 4.488A pdb=" N MET A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 112 through 146 Processing helix chain 'A' and resid 154 through 180 Proline residue: A 175 - end of helix removed outlier: 3.528A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 225 through 245 removed outlier: 3.703A pdb=" N GLN A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 296 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.810A pdb=" N TYR A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.979A pdb=" N PHE A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'B' and resid 7 through 31 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.836A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.616A pdb=" N ASP B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 231' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.845A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 330 through 352 removed outlier: 3.962A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.772A pdb=" N MET D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 60 through 70 removed outlier: 4.458A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.640A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 5.821A pdb=" N THR A 31 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 191 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A 33 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 183 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 202 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU A 200 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N HIS A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N TYR A 198 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 7.101A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 322 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.096A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN C 340 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.621A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.862A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.801A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.024A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 232 removed outlier: 3.632A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.095A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.789A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.738A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.881A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 413 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2913 1.35 - 1.47: 2323 1.47 - 1.60: 3897 1.60 - 1.72: 0 1.72 - 1.84: 102 Bond restraints: 9235 Sorted by residual: bond pdb=" C PHE L 8 " pdb=" N ALA L 9 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" CB MET A 235 " pdb=" CG MET A 235 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" N LYS B 192 " pdb=" CA LYS B 192 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.33e+00 bond pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CB GLU B 289 " pdb=" CG GLU B 289 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.80e-01 ... (remaining 9230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 12168 1.55 - 3.09: 259 3.09 - 4.64: 51 4.64 - 6.18: 23 6.18 - 7.73: 8 Bond angle restraints: 12509 Sorted by residual: angle pdb=" CA ARG A 260 " pdb=" CB ARG A 260 " pdb=" CG ARG A 260 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA LYS B 345 " pdb=" CB LYS B 345 " pdb=" CG LYS B 345 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N ASP C 153 " pdb=" CA ASP C 153 " pdb=" C ASP C 153 " ideal model delta sigma weight residual 108.19 103.85 4.34 1.29e+00 6.01e-01 1.13e+01 angle pdb=" CA CYS A 203 " pdb=" CB CYS A 203 " pdb=" SG CYS A 203 " ideal model delta sigma weight residual 114.40 121.21 -6.81 2.30e+00 1.89e-01 8.75e+00 angle pdb=" CA LYS B 192 " pdb=" CB LYS B 192 " pdb=" CG LYS B 192 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.25e+00 ... (remaining 12504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4628 17.93 - 35.87: 631 35.87 - 53.80: 172 53.80 - 71.73: 34 71.73 - 89.67: 9 Dihedral angle restraints: 5474 sinusoidal: 2135 harmonic: 3339 Sorted by residual: dihedral pdb=" CA PHE L 3 " pdb=" C PHE L 3 " pdb=" N GLN L 4 " pdb=" CA GLN L 4 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU L 2 " pdb=" C LEU L 2 " pdb=" N PHE L 3 " pdb=" CA PHE L 3 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1007 0.040 - 0.080: 280 0.080 - 0.119: 108 0.119 - 0.159: 16 0.159 - 0.199: 2 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA LYS B 192 " pdb=" N LYS B 192 " pdb=" C LYS B 192 " pdb=" CB LYS B 192 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CB VAL A 215 " pdb=" CA VAL A 215 " pdb=" CG1 VAL A 215 " pdb=" CG2 VAL A 215 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1410 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 153 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" CG ASP C 153 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP C 153 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP C 153 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO S 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 3 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PHE L 3 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE L 3 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN L 4 " -0.010 2.00e-02 2.50e+03 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3787 2.93 - 3.42: 8502 3.42 - 3.91: 13873 3.91 - 4.41: 14919 4.41 - 4.90: 25923 Nonbonded interactions: 67004 Sorted by model distance: nonbonded pdb=" OD1 ASP C 153 " pdb=" N ASP C 154 " model vdw 2.432 3.120 nonbonded pdb=" N ASP B 315 " pdb=" OD1 ASP B 315 " model vdw 2.518 3.120 nonbonded pdb=" O LYS C 280 " pdb=" OG SER C 281 " model vdw 2.553 3.040 nonbonded pdb=" O ALA C 257 " pdb=" OE1 GLN C 259 " model vdw 2.553 3.040 nonbonded pdb=" N ASP C 153 " pdb=" O ASP C 153 " model vdw 2.555 2.496 ... (remaining 66999 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: 0.970 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 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 0.055 9236 Z= 0.141 Angle : 0.623 7.729 12511 Z= 0.327 Chirality : 0.043 0.199 1413 Planarity : 0.004 0.050 1579 Dihedral : 17.912 89.666 3311 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.57 % Allowed : 29.54 % Favored : 65.89 % 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: 0.01 (0.25), residues: 1128 helix: 1.27 (0.27), residues: 379 sheet: 0.64 (0.33), residues: 264 loop : -1.41 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 265 TYR 0.017 0.001 TYR S 235 PHE 0.013 0.001 PHE A 66 TRP 0.024 0.001 TRP A 316 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9235) covalent geometry : angle 0.62241 (12509) SS BOND : bond 0.01464 ( 1) SS BOND : angle 2.63306 ( 2) hydrogen bonds : bond 0.18016 ( 413) hydrogen bonds : angle 6.03415 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 TRP cc_start: 0.7457 (OUTLIER) cc_final: 0.7132 (t-100) REVERT: B 22 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7679 (m-40) REVERT: B 25 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 191 PHE cc_start: 0.7746 (t80) cc_final: 0.7149 (t80) REVERT: B 248 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7324 (ttmm) REVERT: B 308 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7159 (mp0) REVERT: B 334 PHE cc_start: 0.6683 (t80) cc_final: 0.6482 (t80) REVERT: B 345 LYS cc_start: 0.7709 (tptp) cc_final: 0.7492 (tppt) REVERT: C 96 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6803 (mtt180) REVERT: C 110 ASN cc_start: 0.8247 (m-40) cc_final: 0.8019 (m110) REVERT: C 252 LEU cc_start: 0.8201 (tt) cc_final: 0.7830 (tp) REVERT: C 273 ILE cc_start: 0.8220 (mt) cc_final: 0.7928 (mt) REVERT: C 280 LYS cc_start: 0.8540 (tttt) cc_final: 0.8329 (mtpt) REVERT: C 327 VAL cc_start: 0.8090 (t) cc_final: 0.7860 (p) REVERT: D 77 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7016 (tptt) REVERT: S 109 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: S 235 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.5431 (t80) outliers start: 45 outliers final: 15 residues processed: 268 average time/residue: 0.0917 time to fit residues: 32.8275 Evaluate side-chains 217 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 79 ASN A 321 ASN B 269 ASN C 266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.173838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140282 restraints weight = 13495.526| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.02 r_work: 0.3658 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9236 Z= 0.132 Angle : 0.585 6.567 12511 Z= 0.306 Chirality : 0.043 0.169 1413 Planarity : 0.004 0.048 1579 Dihedral : 6.273 55.970 1281 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.97 % Allowed : 27.61 % Favored : 67.41 % 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: 0.33 (0.25), residues: 1128 helix: 1.75 (0.27), residues: 381 sheet: 0.72 (0.32), residues: 277 loop : -1.44 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.017 0.001 TYR S 235 PHE 0.025 0.002 PHE B 189 TRP 0.010 0.001 TRP A 287 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9235) covalent geometry : angle 0.58426 (12509) SS BOND : bond 0.00882 ( 1) SS BOND : angle 2.46102 ( 2) hydrogen bonds : bond 0.04435 ( 413) hydrogen bonds : angle 4.36179 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7137 (tp) REVERT: A 181 THR cc_start: 0.5790 (p) cc_final: 0.5582 (p) REVERT: A 212 MET cc_start: 0.4794 (ttm) cc_final: 0.4518 (tpp) REVERT: A 216 TYR cc_start: 0.6737 (t80) cc_final: 0.6478 (t80) REVERT: B 22 ASN cc_start: 0.8163 (t0) cc_final: 0.7765 (m-40) REVERT: B 25 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 33 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7699 (mt-10) REVERT: B 229 ASP cc_start: 0.7748 (m-30) cc_final: 0.6680 (p0) REVERT: B 243 MET cc_start: 0.7555 (mmt) cc_final: 0.6908 (mmt) REVERT: B 248 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7469 (ttmm) REVERT: B 268 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5908 (mt) REVERT: B 270 LYS cc_start: 0.8033 (tppt) cc_final: 0.7606 (mtpt) REVERT: C 32 GLN cc_start: 0.8134 (tp40) cc_final: 0.7890 (tp40) REVERT: C 98 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8221 (p) REVERT: C 127 LYS cc_start: 0.8664 (mttp) cc_final: 0.8353 (mttp) REVERT: C 266 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7462 (t-90) REVERT: C 280 LYS cc_start: 0.8538 (tttt) cc_final: 0.8230 (mtpt) REVERT: S 83 MET cc_start: 0.7487 (mmt) cc_final: 0.7075 (mmt) REVERT: S 109 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: S 139 VAL cc_start: 0.8292 (t) cc_final: 0.8036 (p) REVERT: S 230 MET cc_start: 0.8411 (ttp) cc_final: 0.7982 (ttp) REVERT: S 235 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5605 (t80) outliers start: 49 outliers final: 25 residues processed: 249 average time/residue: 0.0825 time to fit residues: 28.2141 Evaluate side-chains 232 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 321 ASN C 266 HIS C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.159278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126671 restraints weight = 13303.237| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.98 r_work: 0.3507 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9236 Z= 0.236 Angle : 0.699 8.463 12511 Z= 0.373 Chirality : 0.047 0.244 1413 Planarity : 0.005 0.045 1579 Dihedral : 5.681 49.567 1254 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.90 % Allowed : 25.28 % Favored : 67.82 % 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 are not related in a simple way. whole: 0.01 (0.25), residues: 1128 helix: 1.62 (0.27), residues: 381 sheet: 0.56 (0.31), residues: 273 loop : -1.75 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 219 TYR 0.026 0.002 TYR S 190 PHE 0.030 0.002 PHE C 151 TRP 0.016 0.002 TRP C 211 HIS 0.022 0.002 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 9235) covalent geometry : angle 0.69772 (12509) SS BOND : bond 0.01124 ( 1) SS BOND : angle 3.43206 ( 2) hydrogen bonds : bond 0.06243 ( 413) hydrogen bonds : angle 4.69867 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.5073 (m-10) cc_final: 0.4723 (m-10) REVERT: A 170 LEU cc_start: 0.8053 (mm) cc_final: 0.7747 (mt) REVERT: A 198 TYR cc_start: 0.6656 (m-80) cc_final: 0.6431 (m-80) REVERT: A 212 MET cc_start: 0.4785 (ttm) cc_final: 0.4446 (tpp) REVERT: A 213 ARG cc_start: 0.5851 (mmm160) cc_final: 0.5161 (tpp80) REVERT: A 290 LEU cc_start: 0.5887 (mt) cc_final: 0.5486 (tt) REVERT: B 8 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: B 22 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7843 (m-40) REVERT: B 25 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7841 (tp30) REVERT: B 33 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 194 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8338 (mp) REVERT: B 243 MET cc_start: 0.7935 (mmt) cc_final: 0.7490 (mmp) REVERT: B 248 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7734 (ttmm) REVERT: B 275 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: B 308 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7714 (mp0) REVERT: C 96 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6727 (mtt180) REVERT: C 129 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7760 (ttm-80) REVERT: C 138 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 153 ASP cc_start: 0.7949 (t0) cc_final: 0.7748 (t0) REVERT: C 280 LYS cc_start: 0.8607 (tttt) cc_final: 0.8344 (mtpt) REVERT: S 83 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7143 (mmm) REVERT: S 93 MET cc_start: 0.7488 (ttm) cc_final: 0.7120 (ttp) REVERT: S 109 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: S 230 MET cc_start: 0.8556 (ttp) cc_final: 0.8037 (ttp) outliers start: 68 outliers final: 39 residues processed: 248 average time/residue: 0.0817 time to fit residues: 27.7526 Evaluate side-chains 238 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 71 ASN A 73 HIS A 84 ASN A 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125826 restraints weight = 13580.938| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.01 r_work: 0.3507 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9236 Z= 0.177 Angle : 0.613 6.514 12511 Z= 0.327 Chirality : 0.044 0.216 1413 Planarity : 0.004 0.045 1579 Dihedral : 5.113 51.592 1250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.19 % Allowed : 26.60 % Favored : 67.21 % 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: 0.08 (0.25), residues: 1128 helix: 1.70 (0.27), residues: 382 sheet: 0.34 (0.30), residues: 290 loop : -1.62 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.023 0.002 TYR S 235 PHE 0.022 0.002 PHE B 189 TRP 0.014 0.002 TRP C 211 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9235) covalent geometry : angle 0.61269 (12509) SS BOND : bond 0.01199 ( 1) SS BOND : angle 2.50461 ( 2) hydrogen bonds : bond 0.05117 ( 413) hydrogen bonds : angle 4.40458 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7705 (mt) REVERT: A 170 LEU cc_start: 0.8281 (mm) cc_final: 0.8012 (mt) REVERT: A 212 MET cc_start: 0.4986 (ttm) cc_final: 0.3406 (ppp) REVERT: A 290 LEU cc_start: 0.6310 (mt) cc_final: 0.5725 (tt) REVERT: B 8 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6085 (mt-10) REVERT: B 22 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: B 25 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7898 (tp30) REVERT: B 248 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7708 (ttmm) REVERT: B 274 PHE cc_start: 0.5831 (t80) cc_final: 0.5380 (t80) REVERT: B 275 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: B 276 GLU cc_start: 0.6290 (mp0) cc_final: 0.5326 (mp0) REVERT: B 308 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7739 (mp0) REVERT: B 345 LYS cc_start: 0.8420 (tppt) cc_final: 0.8030 (tppt) REVERT: C 23 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7722 (tmmt) REVERT: C 75 GLN cc_start: 0.8867 (mt0) cc_final: 0.8644 (mt0) REVERT: C 129 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7612 (ttm-80) REVERT: C 153 ASP cc_start: 0.7899 (t0) cc_final: 0.7636 (t0) REVERT: C 239 ASN cc_start: 0.8060 (m-40) cc_final: 0.7830 (m110) REVERT: C 280 LYS cc_start: 0.8647 (tttt) cc_final: 0.8398 (mtpt) REVERT: D 50 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7420 (mm) REVERT: S 83 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7173 (mmm) REVERT: S 109 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: S 115 THR cc_start: 0.8010 (t) cc_final: 0.7810 (t) REVERT: S 224 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7918 (m) REVERT: S 230 MET cc_start: 0.8495 (ttp) cc_final: 0.7996 (ttp) outliers start: 61 outliers final: 43 residues processed: 243 average time/residue: 0.0842 time to fit residues: 27.8262 Evaluate side-chains 253 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 71 ASN A 123 GLN B 241 ASN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126716 restraints weight = 13376.866| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.97 r_work: 0.3513 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9236 Z= 0.142 Angle : 0.581 6.699 12511 Z= 0.307 Chirality : 0.043 0.197 1413 Planarity : 0.004 0.045 1579 Dihedral : 4.813 53.770 1248 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.38 % Allowed : 28.02 % Favored : 66.60 % 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 are not related in a simple way. whole: 0.12 (0.25), residues: 1128 helix: 1.80 (0.28), residues: 382 sheet: 0.35 (0.30), residues: 288 loop : -1.64 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 213 TYR 0.020 0.001 TYR S 235 PHE 0.022 0.001 PHE B 189 TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9235) covalent geometry : angle 0.58047 (12509) SS BOND : bond 0.00429 ( 1) SS BOND : angle 2.00806 ( 2) hydrogen bonds : bond 0.04492 ( 413) hydrogen bonds : angle 4.29025 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.6472 (m-80) cc_final: 0.6027 (m-80) REVERT: A 212 MET cc_start: 0.5757 (ttm) cc_final: 0.4010 (ppp) REVERT: A 290 LEU cc_start: 0.6182 (mt) cc_final: 0.5712 (tt) REVERT: A 309 TYR cc_start: 0.5816 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: B 8 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5903 (mt-10) REVERT: B 22 ASN cc_start: 0.8113 (t0) cc_final: 0.7628 (m-40) REVERT: B 25 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 33 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 248 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7722 (ttmm) REVERT: B 274 PHE cc_start: 0.5878 (t80) cc_final: 0.5675 (t80) REVERT: B 275 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: B 298 GLU cc_start: 0.7548 (tp30) cc_final: 0.7211 (tm-30) REVERT: B 308 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7635 (mp0) REVERT: C 23 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7761 (tmmt) REVERT: C 129 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7536 (ttm-80) REVERT: C 153 ASP cc_start: 0.7841 (t0) cc_final: 0.7595 (t0) REVERT: C 280 LYS cc_start: 0.8648 (tttt) cc_final: 0.8390 (mtpt) REVERT: D 50 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7522 (mm) REVERT: S 83 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7112 (mmm) REVERT: S 109 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7440 (m-30) outliers start: 53 outliers final: 37 residues processed: 238 average time/residue: 0.1060 time to fit residues: 33.8806 Evaluate side-chains 245 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126341 restraints weight = 13514.538| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.99 r_work: 0.3510 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.137 Angle : 0.581 6.743 12511 Z= 0.306 Chirality : 0.043 0.196 1413 Planarity : 0.004 0.044 1579 Dihedral : 4.724 55.841 1248 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.89 % Allowed : 28.53 % Favored : 65.58 % 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: 0.23 (0.25), residues: 1128 helix: 1.89 (0.27), residues: 382 sheet: 0.48 (0.30), residues: 291 loop : -1.65 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.019 0.001 TYR S 235 PHE 0.020 0.001 PHE B 189 TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9235) covalent geometry : angle 0.58036 (12509) SS BOND : bond 0.00916 ( 1) SS BOND : angle 1.60935 ( 2) hydrogen bonds : bond 0.04405 ( 413) hydrogen bonds : angle 4.20591 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.6529 (m-80) cc_final: 0.6042 (m-80) REVERT: A 212 MET cc_start: 0.5842 (ttm) cc_final: 0.4139 (ppp) REVERT: A 290 LEU cc_start: 0.6284 (mt) cc_final: 0.5848 (tt) REVERT: A 309 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.5388 (m-80) REVERT: B 22 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7651 (m-40) REVERT: B 36 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 247 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7680 (ptm) REVERT: B 248 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7831 (ttmm) REVERT: B 274 PHE cc_start: 0.5835 (t80) cc_final: 0.5459 (t80) REVERT: B 275 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 276 GLU cc_start: 0.6764 (mp0) cc_final: 0.6466 (mp0) REVERT: B 308 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7685 (mp0) REVERT: C 23 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7808 (tmmt) REVERT: C 129 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7725 (ttm-80) REVERT: C 266 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7416 (t70) REVERT: C 280 LYS cc_start: 0.8653 (tttt) cc_final: 0.8247 (mtpt) REVERT: D 46 LEU cc_start: 0.7880 (tp) cc_final: 0.7673 (tp) REVERT: S 47 TRP cc_start: 0.7909 (t60) cc_final: 0.7694 (t60) REVERT: S 83 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7110 (mmm) REVERT: S 109 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7449 (m-30) outliers start: 58 outliers final: 40 residues processed: 238 average time/residue: 0.1027 time to fit residues: 33.2643 Evaluate side-chains 252 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 91 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126963 restraints weight = 13594.154| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.00 r_work: 0.3524 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.118 Angle : 0.569 6.616 12511 Z= 0.298 Chirality : 0.042 0.194 1413 Planarity : 0.004 0.046 1579 Dihedral : 4.591 57.830 1248 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.77 % Allowed : 29.34 % Favored : 65.89 % 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: 0.33 (0.25), residues: 1128 helix: 1.98 (0.27), residues: 382 sheet: 0.59 (0.30), residues: 286 loop : -1.62 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.017 0.001 TYR S 235 PHE 0.018 0.001 PHE B 189 TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9235) covalent geometry : angle 0.56910 (12509) SS BOND : bond 0.00828 ( 1) SS BOND : angle 1.42741 ( 2) hydrogen bonds : bond 0.03958 ( 413) hydrogen bonds : angle 4.12148 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.5638 (ttm) cc_final: 0.3948 (ppp) REVERT: A 290 LEU cc_start: 0.6246 (mt) cc_final: 0.5867 (tt) REVERT: B 22 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: B 33 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7936 (mt-10) REVERT: B 248 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7797 (ttmm) REVERT: B 274 PHE cc_start: 0.5771 (t80) cc_final: 0.5384 (t80) REVERT: B 275 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: B 276 GLU cc_start: 0.6886 (mp0) cc_final: 0.6622 (mp0) REVERT: B 308 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7639 (mp0) REVERT: B 328 ASP cc_start: 0.7234 (t0) cc_final: 0.6777 (p0) REVERT: C 23 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7785 (tmmt) REVERT: C 129 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: C 266 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7249 (t70) REVERT: S 83 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6926 (mmm) REVERT: S 87 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7694 (mtt180) REVERT: S 109 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7483 (m-30) outliers start: 47 outliers final: 38 residues processed: 231 average time/residue: 0.1029 time to fit residues: 32.2047 Evaluate side-chains 243 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.157028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124897 restraints weight = 13530.334| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.97 r_work: 0.3499 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9236 Z= 0.149 Angle : 0.606 9.104 12511 Z= 0.318 Chirality : 0.043 0.207 1413 Planarity : 0.005 0.089 1579 Dihedral : 4.735 58.809 1248 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.48 % Allowed : 28.63 % Favored : 65.89 % 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: 0.27 (0.25), residues: 1128 helix: 1.96 (0.27), residues: 382 sheet: 0.54 (0.30), residues: 287 loop : -1.68 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 213 TYR 0.024 0.002 TYR S 235 PHE 0.019 0.001 PHE B 189 TRP 0.014 0.001 TRP S 47 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9235) covalent geometry : angle 0.60594 (12509) SS BOND : bond 0.00851 ( 1) SS BOND : angle 1.61923 ( 2) hydrogen bonds : bond 0.04490 ( 413) hydrogen bonds : angle 4.21496 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.6347 (ttm) cc_final: 0.4497 (ppp) REVERT: A 290 LEU cc_start: 0.6267 (mt) cc_final: 0.5928 (tt) REVERT: B 22 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: B 33 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 240 MET cc_start: 0.3406 (ttp) cc_final: 0.2038 (tmm) REVERT: B 248 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7782 (ttmm) REVERT: B 274 PHE cc_start: 0.5880 (t80) cc_final: 0.5502 (t80) REVERT: B 276 GLU cc_start: 0.7104 (mp0) cc_final: 0.6715 (mp0) REVERT: B 308 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7645 (mp0) REVERT: B 328 ASP cc_start: 0.7332 (t0) cc_final: 0.6903 (p0) REVERT: C 23 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7804 (tmmt) REVERT: C 129 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7524 (ttm-80) REVERT: C 246 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8337 (t0) REVERT: C 266 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7135 (t70) REVERT: S 47 TRP cc_start: 0.7794 (t60) cc_final: 0.7531 (t60) REVERT: S 83 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7102 (mmm) REVERT: S 87 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7704 (mtt180) REVERT: S 109 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7465 (m-30) outliers start: 54 outliers final: 42 residues processed: 243 average time/residue: 0.0950 time to fit residues: 32.0966 Evaluate side-chains 260 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.157983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125968 restraints weight = 13493.247| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.00 r_work: 0.3517 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.129 Angle : 0.585 10.026 12511 Z= 0.305 Chirality : 0.043 0.209 1413 Planarity : 0.004 0.068 1579 Dihedral : 4.657 59.776 1248 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.28 % Allowed : 29.24 % Favored : 65.48 % 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: 0.35 (0.25), residues: 1128 helix: 2.01 (0.27), residues: 382 sheet: 0.76 (0.30), residues: 278 loop : -1.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 213 TYR 0.018 0.001 TYR S 235 PHE 0.021 0.001 PHE L 8 TRP 0.011 0.001 TRP B 211 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9235) covalent geometry : angle 0.58442 (12509) SS BOND : bond 0.00795 ( 1) SS BOND : angle 1.40460 ( 2) hydrogen bonds : bond 0.04118 ( 413) hydrogen bonds : angle 4.14114 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.6190 (ttm) cc_final: 0.4266 (ppp) REVERT: A 290 LEU cc_start: 0.6209 (mt) cc_final: 0.5874 (tt) REVERT: B 8 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: B 22 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7627 (m-40) REVERT: B 25 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 248 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7763 (ttmm) REVERT: B 274 PHE cc_start: 0.5914 (t80) cc_final: 0.5710 (t80) REVERT: B 276 GLU cc_start: 0.7291 (mp0) cc_final: 0.7024 (mp0) REVERT: B 308 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7633 (mp0) REVERT: B 328 ASP cc_start: 0.7403 (t0) cc_final: 0.6914 (p0) REVERT: C 23 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7834 (tmmt) REVERT: C 129 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7489 (ttm-80) REVERT: C 266 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7097 (t70) REVERT: S 47 TRP cc_start: 0.7870 (t60) cc_final: 0.7605 (t60) REVERT: S 83 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7036 (mmm) REVERT: S 87 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7725 (mtt180) REVERT: S 109 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7451 (m-30) outliers start: 52 outliers final: 39 residues processed: 245 average time/residue: 0.1057 time to fit residues: 35.1678 Evaluate side-chains 254 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 104 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128848 restraints weight = 13383.863| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.96 r_work: 0.3554 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9236 Z= 0.105 Angle : 0.576 10.829 12511 Z= 0.298 Chirality : 0.042 0.204 1413 Planarity : 0.004 0.053 1579 Dihedral : 4.445 57.839 1248 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.35 % Allowed : 31.37 % Favored : 65.28 % 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: 0.49 (0.25), residues: 1128 helix: 2.10 (0.27), residues: 382 sheet: 0.95 (0.31), residues: 269 loop : -1.62 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.015 0.001 TYR S 235 PHE 0.019 0.001 PHE L 8 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9235) covalent geometry : angle 0.57640 (12509) SS BOND : bond 0.00664 ( 1) SS BOND : angle 0.91776 ( 2) hydrogen bonds : bond 0.03514 ( 413) hydrogen bonds : angle 4.02232 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.6045 (ttm) cc_final: 0.4286 (ppp) REVERT: A 235 MET cc_start: 0.4925 (tmm) cc_final: 0.4647 (tmm) REVERT: A 290 LEU cc_start: 0.6167 (mt) cc_final: 0.5852 (tt) REVERT: B 22 ASN cc_start: 0.8080 (t0) cc_final: 0.7648 (m-40) REVERT: B 248 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7752 (ttmm) REVERT: B 276 GLU cc_start: 0.7260 (mp0) cc_final: 0.6826 (mp0) REVERT: B 308 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7622 (mp0) REVERT: C 23 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7778 (tmmt) REVERT: C 266 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7146 (t70) REVERT: S 83 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6907 (mmm) REVERT: S 87 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7595 (mtt180) REVERT: S 109 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7456 (m-30) outliers start: 33 outliers final: 28 residues processed: 227 average time/residue: 0.0994 time to fit residues: 30.2691 Evaluate side-chains 237 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.158818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126944 restraints weight = 13345.820| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.96 r_work: 0.3519 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9236 Z= 0.125 Angle : 0.607 11.113 12511 Z= 0.312 Chirality : 0.043 0.205 1413 Planarity : 0.004 0.057 1579 Dihedral : 4.516 56.924 1248 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.65 % Allowed : 31.27 % Favored : 65.08 % 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: 0.47 (0.25), residues: 1128 helix: 2.10 (0.27), residues: 381 sheet: 0.90 (0.31), residues: 266 loop : -1.60 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.019 0.001 TYR S 235 PHE 0.018 0.001 PHE B 189 TRP 0.021 0.001 TRP S 47 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9235) covalent geometry : angle 0.60694 (12509) SS BOND : bond 0.00732 ( 1) SS BOND : angle 1.23717 ( 2) hydrogen bonds : bond 0.03922 ( 413) hydrogen bonds : angle 4.04442 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.44 seconds wall clock time: 38 minutes 3.89 seconds (2283.89 seconds total)