Starting phenix.real_space_refine on Tue Mar 3 21:17:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk7_33889/03_2026/7yk7_33889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk7_33889/03_2026/7yk7_33889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yk7_33889/03_2026/7yk7_33889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk7_33889/03_2026/7yk7_33889.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk7_33889/03_2026/7yk7_33889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk7_33889/03_2026/7yk7_33889.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 55 5.16 5 C 5590 2.51 5 N 1495 2.21 5 O 1620 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8760 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1737 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2191 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" 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: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IYM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG R 194 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG R 194 " occ=0.50 Time building chain proxies: 1.87, per 1000 atoms: 0.21 Number of scatterers: 8760 At special positions: 0 Unit cell: (93.177, 118.881, 136.017, 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 55 16.00 O 1620 8.00 N 1495 7.00 C 5590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 319.5 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.716A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.732A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.705A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 32 removed outlier: 3.732A pdb=" N ARG I 32 " --> pdb=" O GLU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.677A pdb=" N MET I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 217 removed outlier: 3.534A pdb=" N CYS I 215 " --> pdb=" O TRP I 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU I 217 " --> pdb=" O HIS I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 275 through 282 removed outlier: 3.501A pdb=" N THR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 331 through 352 Processing helix chain 'R' and resid 37 through 64 removed outlier: 3.589A pdb=" N MET R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 76 No H-bonds generated for 'chain 'R' and resid 74 through 76' Processing helix chain 'R' and resid 77 through 103 Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.743A pdb=" N MET R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 removed outlier: 3.554A pdb=" N VAL R 172 " --> pdb=" O ALA R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.764A pdb=" N PHE R 179 " --> pdb=" O PRO R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 213 removed outlier: 3.663A pdb=" N ALA R 203 " --> pdb=" O TYR R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 233 Processing helix chain 'R' and resid 237 through 273 removed outlier: 3.563A pdb=" N VAL R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) Proline residue: R 261 - end of helix removed outlier: 3.631A pdb=" N VAL R 265 " --> pdb=" O PRO R 261 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS R 273 " --> pdb=" O GLY R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 290 removed outlier: 4.117A pdb=" N GLN R 287 " --> pdb=" O PHE R 283 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 299 Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 322 removed outlier: 3.736A pdb=" N ARG R 317 " --> pdb=" O ARG R 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.190A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.674A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.841A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 25 removed outlier: 3.632A pdb=" N CYS T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'I' and resid 186 through 191 removed outlier: 3.961A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 183 through 184 Processing sheet with id=AA3, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.847A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.602A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.556A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.556A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 47 through 51 removed outlier: 6.863A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 58 through 63 removed outlier: 3.688A pdb=" N ALA T 60 " --> pdb=" O ALA T 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU T 79 " --> pdb=" O ALA T 92 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA T 92 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE T 81 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 100 through 105 removed outlier: 7.021A pdb=" N GLY T 115 " --> pdb=" O MET T 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS T 103 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA T 113 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR T 105 " --> pdb=" O TYR T 111 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR T 111 " --> pdb=" O TYR T 105 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 146 through 151 removed outlier: 3.706A pdb=" N CYS T 148 " --> pdb=" O SER T 160 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 187 through 192 removed outlier: 6.401A pdb=" N GLY T 202 " --> pdb=" O MET T 188 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU T 190 " --> pdb=" O VAL T 200 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL T 200 " --> pdb=" O LEU T 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 229 through 234 removed outlier: 3.634A pdb=" N ALA T 231 " --> pdb=" O GLY T 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET T 262 " --> pdb=" O LEU T 252 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP T 254 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU T 260 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 273 through 278 removed outlier: 6.571A pdb=" N CYS T 294 " --> pdb=" O VAL T 307 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL T 307 " --> pdb=" O CYS T 294 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL T 296 " --> pdb=" O ALA T 305 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1191 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: 1.22 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1412 1.31 - 1.43: 2459 1.43 - 1.56: 5001 1.56 - 1.68: 3 1.68 - 1.81: 78 Bond restraints: 8953 Sorted by residual: bond pdb=" C15 IYM R 401 " pdb=" N14 IYM R 401 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C15 IYM R 401 " pdb=" N17 IYM R 401 " ideal model delta sigma weight residual 1.368 1.470 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C25 IYM R 401 " pdb=" C26 IYM R 401 " ideal model delta sigma weight residual 1.496 1.591 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C24 IYM R 401 " pdb=" C25 IYM R 401 " ideal model delta sigma weight residual 1.528 1.596 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CA ARG I 243 " pdb=" C ARG I 243 " ideal model delta sigma weight residual 1.522 1.484 0.039 1.36e-02 5.41e+03 8.17e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 12007 2.72 - 5.45: 122 5.45 - 8.17: 15 8.17 - 10.89: 4 10.89 - 13.61: 3 Bond angle restraints: 12151 Sorted by residual: angle pdb=" N LEU I 233 " pdb=" CA LEU I 233 " pdb=" C LEU I 233 " ideal model delta sigma weight residual 109.11 95.50 13.61 1.42e+00 4.96e-01 9.19e+01 angle pdb=" N VAL I 234 " pdb=" CA VAL I 234 " pdb=" C VAL I 234 " ideal model delta sigma weight residual 109.34 120.11 -10.77 2.08e+00 2.31e-01 2.68e+01 angle pdb=" C SER R 197 " pdb=" N ARG R 198 " pdb=" CA ARG R 198 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" CA ARG R 198 " pdb=" CB ARG R 198 " pdb=" CG ARG R 198 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" N SER R 197 " pdb=" CA SER R 197 " pdb=" C SER R 197 " ideal model delta sigma weight residual 112.26 107.53 4.73 1.32e+00 5.74e-01 1.29e+01 ... (remaining 12146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.50: 4878 20.50 - 41.00: 357 41.00 - 61.50: 33 61.50 - 81.99: 13 81.99 - 102.49: 2 Dihedral angle restraints: 5283 sinusoidal: 2043 harmonic: 3240 Sorted by residual: dihedral pdb=" CA PRO R 196 " pdb=" C PRO R 196 " pdb=" N SER R 197 " pdb=" CA SER R 197 " ideal model delta harmonic sigma weight residual 180.00 144.50 35.50 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 143.03 -50.03 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA LYS S 163 " pdb=" C LYS S 163 " pdb=" N SER S 164 " pdb=" CA SER S 164 " ideal model delta harmonic sigma weight residual 180.00 152.34 27.66 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 5280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1077 0.056 - 0.113: 276 0.113 - 0.169: 23 0.169 - 0.226: 2 0.226 - 0.282: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA LEU I 233 " pdb=" N LEU I 233 " pdb=" C LEU I 233 " pdb=" CB LEU I 233 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ARG R 198 " pdb=" N ARG R 198 " pdb=" C ARG R 198 " pdb=" CB ARG R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA ILE T 273 " pdb=" N ILE T 273 " pdb=" C ILE T 273 " pdb=" CB ILE T 273 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1376 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 197 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C SER R 197 " 0.054 2.00e-02 2.50e+03 pdb=" O SER R 197 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG R 198 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 289 " -0.010 2.00e-02 2.50e+03 1.32e-02 3.47e+00 pdb=" CG TYR T 289 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR T 289 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR T 289 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR T 289 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR T 289 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR T 289 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 289 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO G 49 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.024 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 144 2.67 - 3.23: 8470 3.23 - 3.79: 13517 3.79 - 4.34: 17509 4.34 - 4.90: 29896 Nonbonded interactions: 69536 Sorted by model distance: nonbonded pdb=" O HIS R 299 " pdb=" OG SER R 302 " model vdw 2.115 3.040 nonbonded pdb=" OD1 ASN R 82 " pdb=" OG1 THR R 162 " model vdw 2.179 3.040 nonbonded pdb=" OE2 GLU I 8 " pdb=" OH TYR S 175 " model vdw 2.188 3.040 nonbonded pdb=" NZ LYS I 272 " pdb=" O THR I 325 " model vdw 2.198 3.120 nonbonded pdb=" O ILE T 58 " pdb=" OG SER T 316 " model vdw 2.236 3.040 ... (remaining 69531 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=0.50 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: 1.080 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.000 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 8955 Z= 0.272 Angle : 0.758 13.615 12155 Z= 0.404 Chirality : 0.047 0.282 1379 Planarity : 0.004 0.043 1533 Dihedral : 13.741 102.493 3187 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.11 % Allowed : 0.85 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.26), residues: 1104 helix: 1.55 (0.27), residues: 377 sheet: -0.44 (0.33), residues: 267 loop : -1.64 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 129 TYR 0.027 0.002 TYR T 289 PHE 0.018 0.002 PHE T 235 TRP 0.024 0.002 TRP R 200 HIS 0.009 0.001 HIS T 183 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 8953) covalent geometry : angle 0.75789 (12151) SS BOND : bond 0.00618 ( 2) SS BOND : angle 1.38023 ( 4) hydrogen bonds : bond 0.19496 ( 413) hydrogen bonds : angle 7.31149 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: I 43 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: I 272 LYS cc_start: 0.8073 (pttm) cc_final: 0.7658 (pmtt) REVERT: R 249 ARG cc_start: 0.6839 (tpm170) cc_final: 0.6605 (tpm170) REVERT: S 220 GLU cc_start: 0.7335 (mp0) cc_final: 0.6714 (mp0) REVERT: S 224 VAL cc_start: 0.8272 (t) cc_final: 0.7994 (p) REVERT: T 38 ASP cc_start: 0.7523 (p0) cc_final: 0.7226 (p0) REVERT: T 50 THR cc_start: 0.8574 (m) cc_final: 0.8251 (t) REVERT: T 61 MET cc_start: 0.7240 (ppp) cc_final: 0.6943 (ppp) REVERT: T 76 ASP cc_start: 0.6688 (p0) cc_final: 0.6458 (p0) REVERT: T 96 ARG cc_start: 0.6727 (mtt90) cc_final: 0.6502 (mtt90) REVERT: T 97 SER cc_start: 0.8130 (t) cc_final: 0.7806 (t) REVERT: T 120 ILE cc_start: 0.8055 (mp) cc_final: 0.7846 (mt) REVERT: T 227 SER cc_start: 0.7930 (m) cc_final: 0.7544 (m) REVERT: T 247 ASP cc_start: 0.6710 (m-30) cc_final: 0.6370 (m-30) REVERT: T 254 ASP cc_start: 0.7136 (t70) cc_final: 0.6927 (t70) REVERT: T 268 ASN cc_start: 0.7131 (t0) cc_final: 0.6919 (t0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.5691 time to fit residues: 129.8987 Evaluate side-chains 197 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 ASN R 305 ASN T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.145288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.128099 restraints weight = 12598.678| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.19 r_work: 0.3688 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8955 Z= 0.140 Angle : 0.665 12.570 12155 Z= 0.332 Chirality : 0.044 0.160 1379 Planarity : 0.004 0.037 1533 Dihedral : 7.289 78.876 1248 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.92 % Allowed : 10.98 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1104 helix: 1.62 (0.27), residues: 383 sheet: -0.21 (0.32), residues: 278 loop : -1.53 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 233 TYR 0.013 0.001 TYR R 309 PHE 0.024 0.002 PHE R 230 TRP 0.015 0.001 TRP T 82 HIS 0.006 0.001 HIS T 183 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8953) covalent geometry : angle 0.66510 (12151) SS BOND : bond 0.00581 ( 2) SS BOND : angle 1.25375 ( 4) hydrogen bonds : bond 0.04543 ( 413) hydrogen bonds : angle 5.09934 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7994 (ttmm) REVERT: I 43 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: I 272 LYS cc_start: 0.8526 (pttm) cc_final: 0.7937 (pmtt) REVERT: I 307 LYS cc_start: 0.6109 (mptt) cc_final: 0.5610 (mmtm) REVERT: R 209 VAL cc_start: 0.7780 (p) cc_final: 0.7487 (t) REVERT: R 249 ARG cc_start: 0.7604 (tpm170) cc_final: 0.7309 (tpm170) REVERT: S 192 MET cc_start: 0.5431 (tpt) cc_final: 0.5120 (tpt) REVERT: S 220 GLU cc_start: 0.7902 (mp0) cc_final: 0.7396 (mp0) REVERT: T 38 ASP cc_start: 0.7925 (p0) cc_final: 0.7591 (p0) REVERT: T 97 SER cc_start: 0.8340 (t) cc_final: 0.8121 (p) REVERT: T 227 SER cc_start: 0.8605 (m) cc_final: 0.8209 (m) REVERT: T 247 ASP cc_start: 0.7380 (m-30) cc_final: 0.7015 (m-30) REVERT: T 254 ASP cc_start: 0.8051 (t70) cc_final: 0.7795 (t70) REVERT: T 258 ASP cc_start: 0.7439 (t0) cc_final: 0.7043 (t0) REVERT: T 268 ASN cc_start: 0.7484 (t0) cc_final: 0.7257 (t0) REVERT: T 270 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8166 (pp) outliers start: 18 outliers final: 8 residues processed: 206 average time/residue: 0.4945 time to fit residues: 109.2015 Evaluate side-chains 197 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.0370 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 HIS T 155 ASN T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.145654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128576 restraints weight = 12463.698| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.17 r_work: 0.3694 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8955 Z= 0.133 Angle : 0.625 10.552 12155 Z= 0.313 Chirality : 0.043 0.152 1379 Planarity : 0.004 0.039 1533 Dihedral : 6.639 63.013 1248 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.77 % Allowed : 16.10 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1104 helix: 1.78 (0.27), residues: 380 sheet: 0.07 (0.33), residues: 259 loop : -1.57 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 191 TYR 0.015 0.001 TYR R 309 PHE 0.026 0.001 PHE R 230 TRP 0.015 0.001 TRP T 82 HIS 0.005 0.001 HIS T 183 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8953) covalent geometry : angle 0.62517 (12151) SS BOND : bond 0.00650 ( 2) SS BOND : angle 1.07202 ( 4) hydrogen bonds : bond 0.04039 ( 413) hydrogen bonds : angle 4.70048 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8040 (ttmm) REVERT: I 33 GLU cc_start: 0.7550 (tp30) cc_final: 0.7161 (tp30) REVERT: I 226 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8015 (m) REVERT: I 272 LYS cc_start: 0.8496 (pttm) cc_final: 0.7962 (pmtt) REVERT: I 307 LYS cc_start: 0.6281 (mptt) cc_final: 0.6044 (mptt) REVERT: R 198 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5479 (pmt-80) REVERT: R 209 VAL cc_start: 0.7742 (p) cc_final: 0.7450 (t) REVERT: R 249 ARG cc_start: 0.7544 (tpm170) cc_final: 0.7219 (tpm170) REVERT: S 174 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.8000 (tp) REVERT: S 220 GLU cc_start: 0.7910 (mp0) cc_final: 0.7473 (mp0) REVERT: T 38 ASP cc_start: 0.7924 (p0) cc_final: 0.7581 (p0) REVERT: T 97 SER cc_start: 0.8351 (t) cc_final: 0.8109 (p) REVERT: T 222 PHE cc_start: 0.8584 (m-80) cc_final: 0.8348 (m-80) REVERT: T 227 SER cc_start: 0.8656 (m) cc_final: 0.8240 (m) REVERT: T 237 ASN cc_start: 0.8099 (t0) cc_final: 0.7757 (t0) REVERT: T 239 ASN cc_start: 0.8398 (m-40) cc_final: 0.8080 (m110) REVERT: T 247 ASP cc_start: 0.7375 (m-30) cc_final: 0.6990 (m-30) REVERT: T 268 ASN cc_start: 0.7479 (t0) cc_final: 0.7235 (t0) REVERT: T 270 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (pp) outliers start: 26 outliers final: 8 residues processed: 210 average time/residue: 0.4514 time to fit residues: 102.4916 Evaluate side-chains 200 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 198 ARG Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 333 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.0370 chunk 102 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 110 ASN T 119 ASN T 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127263 restraints weight = 12679.779| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.20 r_work: 0.3680 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8955 Z= 0.150 Angle : 0.640 12.659 12155 Z= 0.317 Chirality : 0.044 0.177 1379 Planarity : 0.004 0.038 1533 Dihedral : 6.139 55.739 1245 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.41 % Allowed : 17.80 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1104 helix: 1.88 (0.27), residues: 375 sheet: -0.00 (0.32), residues: 269 loop : -1.52 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 129 TYR 0.013 0.001 TYR R 309 PHE 0.020 0.001 PHE R 230 TRP 0.019 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8953) covalent geometry : angle 0.63945 (12151) SS BOND : bond 0.00726 ( 2) SS BOND : angle 1.11271 ( 4) hydrogen bonds : bond 0.03985 ( 413) hydrogen bonds : angle 4.57047 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8049 (ttmm) REVERT: I 33 GLU cc_start: 0.7590 (tp30) cc_final: 0.7213 (tp30) REVERT: I 226 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8010 (m) REVERT: I 272 LYS cc_start: 0.8531 (pttm) cc_final: 0.7988 (pmtt) REVERT: I 307 LYS cc_start: 0.6265 (mptt) cc_final: 0.5968 (mmtp) REVERT: R 209 VAL cc_start: 0.7726 (p) cc_final: 0.7438 (t) REVERT: R 230 PHE cc_start: 0.8059 (t80) cc_final: 0.7802 (t80) REVERT: S 6 GLU cc_start: 0.7304 (pm20) cc_final: 0.7045 (pm20) REVERT: S 174 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7972 (tp) REVERT: S 220 GLU cc_start: 0.7946 (mp0) cc_final: 0.7550 (mp0) REVERT: T 22 ARG cc_start: 0.7475 (ttm170) cc_final: 0.7175 (ttm170) REVERT: T 96 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7472 (mtt90) REVERT: T 222 PHE cc_start: 0.8599 (m-80) cc_final: 0.8344 (m-80) REVERT: T 227 SER cc_start: 0.8658 (m) cc_final: 0.8229 (m) REVERT: T 237 ASN cc_start: 0.8131 (t0) cc_final: 0.7813 (t0) REVERT: T 239 ASN cc_start: 0.8448 (m-40) cc_final: 0.8185 (m110) REVERT: T 247 ASP cc_start: 0.7346 (m-30) cc_final: 0.6958 (m-30) REVERT: T 258 ASP cc_start: 0.7492 (t0) cc_final: 0.7213 (t0) REVERT: T 268 ASN cc_start: 0.7502 (t0) cc_final: 0.7252 (t0) REVERT: T 270 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8138 (pp) REVERT: T 316 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8065 (m) outliers start: 32 outliers final: 11 residues processed: 220 average time/residue: 0.4166 time to fit residues: 99.5230 Evaluate side-chains 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 110 ASN T 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.126187 restraints weight = 12595.521| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.18 r_work: 0.3662 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8955 Z= 0.192 Angle : 0.653 11.112 12155 Z= 0.329 Chirality : 0.045 0.150 1379 Planarity : 0.004 0.040 1533 Dihedral : 6.096 51.494 1245 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.05 % Allowed : 19.30 % Favored : 76.65 % 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 (0.26), residues: 1104 helix: 1.74 (0.27), residues: 378 sheet: 0.01 (0.32), residues: 271 loop : -1.51 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 129 TYR 0.015 0.002 TYR S 190 PHE 0.017 0.002 PHE R 230 TRP 0.018 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8953) covalent geometry : angle 0.65268 (12151) SS BOND : bond 0.00831 ( 2) SS BOND : angle 1.11680 ( 4) hydrogen bonds : bond 0.04213 ( 413) hydrogen bonds : angle 4.60414 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8067 (ttmm) REVERT: I 33 GLU cc_start: 0.7566 (tp30) cc_final: 0.7345 (tp30) REVERT: I 199 MET cc_start: 0.8354 (mtp) cc_final: 0.8105 (mtm) REVERT: I 226 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8052 (m) REVERT: I 272 LYS cc_start: 0.8593 (pttm) cc_final: 0.8046 (pmtt) REVERT: I 307 LYS cc_start: 0.6314 (mptt) cc_final: 0.6096 (mmtt) REVERT: R 209 VAL cc_start: 0.7732 (p) cc_final: 0.7440 (t) REVERT: S 174 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (tp) REVERT: S 177 PHE cc_start: 0.8339 (m-10) cc_final: 0.8074 (m-80) REVERT: S 220 GLU cc_start: 0.7909 (mp0) cc_final: 0.7508 (mp0) REVERT: T 22 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7250 (ttm170) REVERT: T 96 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7443 (mtt90) REVERT: T 155 ASN cc_start: 0.7914 (t0) cc_final: 0.7711 (t0) REVERT: T 222 PHE cc_start: 0.8635 (m-80) cc_final: 0.8374 (m-80) REVERT: T 226 GLU cc_start: 0.7738 (pm20) cc_final: 0.7497 (pm20) REVERT: T 227 SER cc_start: 0.8624 (m) cc_final: 0.8147 (m) REVERT: T 247 ASP cc_start: 0.7360 (m-30) cc_final: 0.6978 (m-30) REVERT: T 258 ASP cc_start: 0.7511 (t0) cc_final: 0.7239 (t0) REVERT: T 268 ASN cc_start: 0.7508 (t0) cc_final: 0.7248 (t0) REVERT: T 270 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8130 (pp) REVERT: T 316 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.8042 (m) outliers start: 38 outliers final: 22 residues processed: 211 average time/residue: 0.4417 time to fit residues: 100.9667 Evaluate side-chains 210 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 66 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 107 optimal weight: 0.0010 chunk 106 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 110 ASN T 175 GLN T 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.128801 restraints weight = 12768.850| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.19 r_work: 0.3701 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8955 Z= 0.117 Angle : 0.627 14.199 12155 Z= 0.308 Chirality : 0.043 0.152 1379 Planarity : 0.004 0.042 1533 Dihedral : 5.826 50.304 1245 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.30 % Allowed : 21.54 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1104 helix: 2.00 (0.28), residues: 375 sheet: 0.13 (0.33), residues: 268 loop : -1.46 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 129 TYR 0.013 0.001 TYR S 60 PHE 0.015 0.001 PHE R 230 TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS T 183 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8953) covalent geometry : angle 0.62662 (12151) SS BOND : bond 0.00642 ( 2) SS BOND : angle 0.92123 ( 4) hydrogen bonds : bond 0.03612 ( 413) hydrogen bonds : angle 4.39881 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8050 (ttmm) REVERT: I 33 GLU cc_start: 0.7592 (tp30) cc_final: 0.7236 (tp30) REVERT: I 226 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7989 (m) REVERT: I 232 ASP cc_start: 0.8234 (p0) cc_final: 0.8020 (p0) REVERT: I 272 LYS cc_start: 0.8576 (pttm) cc_final: 0.8042 (pmtt) REVERT: R 209 VAL cc_start: 0.7611 (p) cc_final: 0.7304 (t) REVERT: S 174 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7948 (tp) REVERT: S 220 GLU cc_start: 0.7912 (mp0) cc_final: 0.7566 (mp0) REVERT: T 22 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7092 (ttm170) REVERT: T 96 ARG cc_start: 0.7732 (mtt90) cc_final: 0.7371 (mtt90) REVERT: T 155 ASN cc_start: 0.7910 (t0) cc_final: 0.7697 (t0) REVERT: T 226 GLU cc_start: 0.7677 (pm20) cc_final: 0.7466 (pm20) REVERT: T 227 SER cc_start: 0.8597 (m) cc_final: 0.8100 (m) REVERT: T 247 ASP cc_start: 0.7338 (m-30) cc_final: 0.6951 (m-30) REVERT: T 258 ASP cc_start: 0.7549 (t0) cc_final: 0.7129 (t0) REVERT: T 268 ASN cc_start: 0.7507 (t0) cc_final: 0.7228 (t0) REVERT: T 270 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8097 (pp) outliers start: 31 outliers final: 16 residues processed: 204 average time/residue: 0.4401 time to fit residues: 97.2001 Evaluate side-chains 195 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 198 ARG Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.145694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128548 restraints weight = 12643.246| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.18 r_work: 0.3694 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8955 Z= 0.132 Angle : 0.637 13.033 12155 Z= 0.314 Chirality : 0.043 0.150 1379 Planarity : 0.004 0.046 1533 Dihedral : 5.714 48.703 1245 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.77 % Allowed : 24.41 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1104 helix: 2.10 (0.27), residues: 370 sheet: 0.18 (0.32), residues: 269 loop : -1.50 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 129 TYR 0.013 0.001 TYR S 60 PHE 0.016 0.001 PHE R 195 TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8953) covalent geometry : angle 0.63724 (12151) SS BOND : bond 0.00641 ( 2) SS BOND : angle 1.07828 ( 4) hydrogen bonds : bond 0.03683 ( 413) hydrogen bonds : angle 4.38035 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8034 (ttmm) REVERT: I 33 GLU cc_start: 0.7618 (tp30) cc_final: 0.7260 (tp30) REVERT: I 226 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8002 (m) REVERT: R 209 VAL cc_start: 0.7613 (p) cc_final: 0.7316 (t) REVERT: S 174 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7887 (tp) REVERT: S 220 GLU cc_start: 0.7846 (mp0) cc_final: 0.7493 (mp0) REVERT: T 22 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7093 (ttm170) REVERT: T 96 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7405 (mtt90) REVERT: T 222 PHE cc_start: 0.8645 (m-80) cc_final: 0.8382 (m-80) REVERT: T 227 SER cc_start: 0.8586 (m) cc_final: 0.8090 (m) REVERT: T 247 ASP cc_start: 0.7288 (m-30) cc_final: 0.6892 (m-30) REVERT: T 258 ASP cc_start: 0.7492 (t0) cc_final: 0.7105 (t0) REVERT: T 268 ASN cc_start: 0.7519 (t0) cc_final: 0.7237 (t0) REVERT: T 270 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8129 (pp) REVERT: T 316 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.8074 (m) outliers start: 26 outliers final: 14 residues processed: 189 average time/residue: 0.4659 time to fit residues: 95.0977 Evaluate side-chains 189 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127002 restraints weight = 12538.667| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.17 r_work: 0.3671 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8955 Z= 0.171 Angle : 0.654 11.501 12155 Z= 0.326 Chirality : 0.045 0.151 1379 Planarity : 0.004 0.042 1533 Dihedral : 5.681 48.892 1245 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.62 % Allowed : 23.77 % Favored : 72.60 % 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: 0.22 (0.26), residues: 1104 helix: 2.05 (0.27), residues: 368 sheet: 0.20 (0.32), residues: 271 loop : -1.50 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 129 TYR 0.015 0.001 TYR S 190 PHE 0.027 0.002 PHE S 212 TRP 0.017 0.001 TRP T 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8953) covalent geometry : angle 0.65398 (12151) SS BOND : bond 0.00778 ( 2) SS BOND : angle 1.11268 ( 4) hydrogen bonds : bond 0.03948 ( 413) hydrogen bonds : angle 4.45192 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 33 GLU cc_start: 0.7578 (tp30) cc_final: 0.7228 (tp30) REVERT: I 199 MET cc_start: 0.8364 (mtp) cc_final: 0.8123 (mtm) REVERT: I 226 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8049 (m) REVERT: I 233 LEU cc_start: 0.8475 (mt) cc_final: 0.8260 (mm) REVERT: I 272 LYS cc_start: 0.8663 (pttm) cc_final: 0.8123 (pmtt) REVERT: R 209 VAL cc_start: 0.7689 (p) cc_final: 0.7402 (t) REVERT: S 68 PHE cc_start: 0.8437 (m-10) cc_final: 0.8202 (m-10) REVERT: S 174 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7935 (tp) REVERT: S 177 PHE cc_start: 0.8341 (m-10) cc_final: 0.7845 (m-80) REVERT: S 220 GLU cc_start: 0.7907 (mp0) cc_final: 0.7539 (mp0) REVERT: T 22 ARG cc_start: 0.7527 (ttm170) cc_final: 0.7126 (ttm170) REVERT: T 96 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7445 (mtt90) REVERT: T 222 PHE cc_start: 0.8646 (m-80) cc_final: 0.8391 (m-80) REVERT: T 227 SER cc_start: 0.8588 (m) cc_final: 0.8074 (m) REVERT: T 247 ASP cc_start: 0.7376 (m-30) cc_final: 0.6955 (m-30) REVERT: T 258 ASP cc_start: 0.7560 (t0) cc_final: 0.7173 (t0) REVERT: T 268 ASN cc_start: 0.7507 (t0) cc_final: 0.7231 (t0) REVERT: T 270 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8119 (pp) REVERT: T 316 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8064 (m) outliers start: 34 outliers final: 20 residues processed: 214 average time/residue: 0.4971 time to fit residues: 114.2098 Evaluate side-chains 217 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 198 ARG Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 285 LEU Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.0980 chunk 90 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.0010 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.146758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129316 restraints weight = 12710.624| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.20 r_work: 0.3706 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8955 Z= 0.115 Angle : 0.630 13.647 12155 Z= 0.310 Chirality : 0.043 0.148 1379 Planarity : 0.004 0.041 1533 Dihedral : 5.391 48.645 1245 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.56 % Allowed : 24.84 % Favored : 72.60 % 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: 0.37 (0.26), residues: 1104 helix: 2.17 (0.28), residues: 369 sheet: 0.32 (0.33), residues: 268 loop : -1.43 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 129 TYR 0.010 0.001 TYR R 309 PHE 0.024 0.001 PHE S 212 TRP 0.014 0.001 TRP T 82 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8953) covalent geometry : angle 0.62975 (12151) SS BOND : bond 0.00642 ( 2) SS BOND : angle 0.93364 ( 4) hydrogen bonds : bond 0.03446 ( 413) hydrogen bonds : angle 4.30976 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 33 GLU cc_start: 0.7597 (tp30) cc_final: 0.7235 (tp30) REVERT: I 233 LEU cc_start: 0.8464 (mt) cc_final: 0.8256 (mm) REVERT: I 272 LYS cc_start: 0.8650 (pttm) cc_final: 0.8085 (pmtt) REVERT: I 306 SER cc_start: 0.8031 (t) cc_final: 0.7823 (p) REVERT: R 209 VAL cc_start: 0.7554 (p) cc_final: 0.7232 (t) REVERT: S 174 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7888 (tp) REVERT: S 219 LEU cc_start: 0.8317 (mt) cc_final: 0.8110 (mp) REVERT: S 220 GLU cc_start: 0.7802 (mp0) cc_final: 0.7484 (mp0) REVERT: T 22 ARG cc_start: 0.7444 (ttm170) cc_final: 0.7082 (ttm170) REVERT: T 96 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7432 (mtt90) REVERT: T 118 ASP cc_start: 0.7273 (p0) cc_final: 0.7048 (p0) REVERT: T 222 PHE cc_start: 0.8662 (m-80) cc_final: 0.8401 (m-80) REVERT: T 227 SER cc_start: 0.8576 (m) cc_final: 0.8109 (m) REVERT: T 247 ASP cc_start: 0.7268 (m-30) cc_final: 0.6863 (m-30) REVERT: T 258 ASP cc_start: 0.7475 (t0) cc_final: 0.7135 (t0) REVERT: T 268 ASN cc_start: 0.7489 (t0) cc_final: 0.7248 (t0) REVERT: T 270 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8096 (pp) REVERT: T 316 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8049 (m) outliers start: 24 outliers final: 16 residues processed: 194 average time/residue: 0.5377 time to fit residues: 111.2067 Evaluate side-chains 198 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 256 ASN T 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127834 restraints weight = 12634.378| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.18 r_work: 0.3682 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8955 Z= 0.153 Angle : 0.662 13.208 12155 Z= 0.327 Chirality : 0.044 0.152 1379 Planarity : 0.004 0.045 1533 Dihedral : 5.398 47.588 1245 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.13 % Allowed : 25.80 % Favored : 72.07 % 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: 0.34 (0.26), residues: 1104 helix: 2.14 (0.27), residues: 370 sheet: 0.30 (0.32), residues: 276 loop : -1.48 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 129 TYR 0.014 0.001 TYR S 60 PHE 0.024 0.002 PHE S 212 TRP 0.017 0.001 TRP T 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8953) covalent geometry : angle 0.66144 (12151) SS BOND : bond 0.00733 ( 2) SS BOND : angle 1.13013 ( 4) hydrogen bonds : bond 0.03727 ( 413) hydrogen bonds : angle 4.37931 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 33 GLU cc_start: 0.7587 (tp30) cc_final: 0.7247 (tp30) REVERT: I 199 MET cc_start: 0.8382 (mtp) cc_final: 0.8130 (mtm) REVERT: I 272 LYS cc_start: 0.8679 (pttm) cc_final: 0.8091 (pmtt) REVERT: R 209 VAL cc_start: 0.7630 (p) cc_final: 0.7319 (t) REVERT: S 68 PHE cc_start: 0.8391 (m-10) cc_final: 0.8127 (m-10) REVERT: S 80 PHE cc_start: 0.8141 (m-80) cc_final: 0.7913 (m-80) REVERT: S 174 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7951 (tp) REVERT: S 220 GLU cc_start: 0.7881 (mp0) cc_final: 0.7527 (mp0) REVERT: T 22 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7074 (ttm170) REVERT: T 96 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7467 (mtt90) REVERT: T 118 ASP cc_start: 0.7276 (p0) cc_final: 0.7043 (p0) REVERT: T 222 PHE cc_start: 0.8649 (m-80) cc_final: 0.8395 (m-80) REVERT: T 227 SER cc_start: 0.8673 (m) cc_final: 0.8250 (m) REVERT: T 258 ASP cc_start: 0.7529 (t0) cc_final: 0.7203 (t0) REVERT: T 268 ASN cc_start: 0.7522 (t0) cc_final: 0.7267 (t0) REVERT: T 270 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8124 (pp) REVERT: T 316 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.8013 (m) outliers start: 20 outliers final: 16 residues processed: 207 average time/residue: 0.5221 time to fit residues: 115.5424 Evaluate side-chains 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 319 GLU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 198 ARG Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 198 LEU Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 316 SER Chi-restraints excluded: chain T residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.145820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.128523 restraints weight = 12519.961| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.18 r_work: 0.3693 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8955 Z= 0.138 Angle : 0.656 12.602 12155 Z= 0.323 Chirality : 0.044 0.151 1379 Planarity : 0.004 0.047 1533 Dihedral : 5.351 47.953 1245 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.35 % Allowed : 25.37 % Favored : 72.28 % 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: 0.44 (0.26), residues: 1104 helix: 2.41 (0.27), residues: 355 sheet: 0.36 (0.32), residues: 274 loop : -1.46 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 129 TYR 0.010 0.001 TYR R 309 PHE 0.010 0.001 PHE T 151 TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8953) covalent geometry : angle 0.65615 (12151) SS BOND : bond 0.00747 ( 2) SS BOND : angle 1.12625 ( 4) hydrogen bonds : bond 0.03618 ( 413) hydrogen bonds : angle 4.36051 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.17 seconds wall clock time: 66 minutes 15.28 seconds (3975.28 seconds total)