Starting phenix.real_space_refine on Sat Jul 26 17:57:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk7_33889/07_2025/7yk7_33889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk7_33889/07_2025/7yk7_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_33889/07_2025/7yk7_33889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk7_33889/07_2025/7yk7_33889.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk7_33889/07_2025/7yk7_33889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk7_33889/07_2025/7yk7_33889.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.67, per 1000 atoms: 0.65 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: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.00 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: 2.46 Time building geometry restraints manager: 2.75 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: 1.300 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- 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 : 9.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP R 200 HIS 0.009 0.001 HIS T 183 PHE 0.018 0.002 PHE T 235 TYR 0.027 0.002 TYR T 289 ARG 0.009 0.001 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.19496 ( 413) hydrogen bonds : angle 7.31149 ( 1191) SS BOND : bond 0.00618 ( 2) SS BOND : angle 1.38023 ( 4) covalent geometry : bond 0.00598 ( 8953) covalent geometry : angle 0.75789 (12151) *********************** 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 : 0.955 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: 1.1934 time to fit residues: 273.0730 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 : 0.924 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 305 ASN T 175 GLN T 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.144120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127055 restraints weight = 12557.384| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.17 r_work: 0.3675 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8955 Z= 0.168 Angle : 0.680 12.582 12155 Z= 0.342 Chirality : 0.045 0.160 1379 Planarity : 0.004 0.039 1533 Dihedral : 7.380 80.271 1248 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.24 % Allowed : 10.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1104 helix: 1.54 (0.27), residues: 383 sheet: -0.16 (0.32), residues: 268 loop : -1.58 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.006 0.001 HIS T 183 PHE 0.024 0.002 PHE R 230 TYR 0.016 0.001 TYR R 309 ARG 0.007 0.001 ARG R 233 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 413) hydrogen bonds : angle 5.14678 ( 1191) SS BOND : bond 0.00711 ( 2) SS BOND : angle 1.27479 ( 4) covalent geometry : bond 0.00382 ( 8953) covalent geometry : angle 0.68006 (12151) *********************** 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 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8043 (ttmm) REVERT: I 33 GLU cc_start: 0.7578 (tp30) cc_final: 0.7189 (tp30) REVERT: I 43 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: I 198 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7787 (mtpm) REVERT: I 272 LYS cc_start: 0.8518 (pttm) cc_final: 0.7943 (pmtt) REVERT: I 307 LYS cc_start: 0.6059 (mptt) cc_final: 0.5443 (mmtm) REVERT: R 209 VAL cc_start: 0.7794 (p) cc_final: 0.7512 (t) REVERT: R 249 ARG cc_start: 0.7610 (tpm170) cc_final: 0.7334 (tpm170) REVERT: S 192 MET cc_start: 0.5592 (tpt) cc_final: 0.5232 (tpt) REVERT: S 220 GLU cc_start: 0.7882 (mp0) cc_final: 0.7386 (mp0) REVERT: T 38 ASP cc_start: 0.7931 (p0) cc_final: 0.7601 (p0) REVERT: T 96 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7403 (mtt90) REVERT: T 97 SER cc_start: 0.8358 (t) cc_final: 0.8131 (p) REVERT: T 227 SER cc_start: 0.8575 (m) cc_final: 0.8206 (m) REVERT: T 247 ASP cc_start: 0.7401 (m-30) cc_final: 0.7017 (m-30) REVERT: T 254 ASP cc_start: 0.8027 (t70) cc_final: 0.7781 (t70) REVERT: T 258 ASP cc_start: 0.7447 (t0) cc_final: 0.7090 (t0) REVERT: T 268 ASN cc_start: 0.7465 (t0) cc_final: 0.7253 (t0) REVERT: T 270 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8177 (pp) outliers start: 21 outliers final: 11 residues processed: 201 average time/residue: 1.1153 time to fit residues: 240.1833 Evaluate side-chains 209 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 312 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 74 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 ASN 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 = 0.3994 r_free = 0.3994 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126261 restraints weight = 12608.832| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.18 r_work: 0.3666 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8955 Z= 0.182 Angle : 0.661 15.013 12155 Z= 0.330 Chirality : 0.045 0.152 1379 Planarity : 0.004 0.038 1533 Dihedral : 6.767 64.040 1248 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.88 % Allowed : 15.78 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1104 helix: 1.64 (0.27), residues: 379 sheet: -0.03 (0.32), residues: 269 loop : -1.63 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 82 HIS 0.006 0.001 HIS T 183 PHE 0.026 0.002 PHE R 230 TYR 0.018 0.002 TYR R 309 ARG 0.007 0.001 ARG S 191 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 413) hydrogen bonds : angle 4.81985 ( 1191) SS BOND : bond 0.00781 ( 2) SS BOND : angle 1.15619 ( 4) covalent geometry : bond 0.00421 ( 8953) covalent geometry : angle 0.66104 (12151) *********************** 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 236 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8052 (ttmm) REVERT: I 33 GLU cc_start: 0.7557 (tp30) cc_final: 0.7187 (tp30) REVERT: I 198 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7761 (mtpm) REVERT: I 199 MET cc_start: 0.8372 (mtp) cc_final: 0.8101 (mtm) REVERT: I 272 LYS cc_start: 0.8542 (pttm) cc_final: 0.8007 (pmtt) REVERT: I 307 LYS cc_start: 0.6430 (mptt) cc_final: 0.5963 (mmtp) REVERT: R 249 ARG cc_start: 0.7551 (tpm170) cc_final: 0.7276 (tpm170) REVERT: S 174 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7972 (tp) REVERT: S 220 GLU cc_start: 0.7914 (mp0) cc_final: 0.7431 (mp0) REVERT: T 96 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7493 (mtt90) REVERT: T 97 SER cc_start: 0.8372 (t) cc_final: 0.8170 (p) REVERT: T 197 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7934 (ttp80) REVERT: T 227 SER cc_start: 0.8641 (m) cc_final: 0.8226 (m) REVERT: T 268 ASN cc_start: 0.7493 (t0) cc_final: 0.7261 (t0) REVERT: T 270 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8147 (pp) outliers start: 27 outliers final: 10 residues processed: 220 average time/residue: 1.0249 time to fit residues: 242.2314 Evaluate side-chains 205 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 267 LEU Chi-restraints excluded: chain R residue 285 THR 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 270 ILE Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 45 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 HIS T 110 ASN T 119 ASN T 155 ASN T 175 GLN T 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127552 restraints weight = 12530.282| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.18 r_work: 0.3683 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- 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 = 0.97 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 = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1741 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= 0.137 Angle : 0.635 15.005 12155 Z= 0.314 Chirality : 0.044 0.195 1379 Planarity : 0.004 0.037 1533 Dihedral : 6.163 54.800 1245 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.73 % Allowed : 17.38 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1104 helix: 1.79 (0.27), residues: 379 sheet: 0.07 (0.32), residues: 273 loop : -1.56 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 82 HIS 0.004 0.001 HIS T 183 PHE 0.020 0.001 PHE R 230 TYR 0.013 0.001 TYR R 309 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 413) hydrogen bonds : angle 4.60982 ( 1191) SS BOND : bond 0.00761 ( 2) SS BOND : angle 1.02423 ( 4) covalent geometry : bond 0.00313 ( 8953) covalent geometry : angle 0.63518 (12151) *********************** 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 236 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: I 26 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: I 29 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8044 (ttmm) REVERT: I 33 GLU cc_start: 0.7598 (tp30) cc_final: 0.7233 (tp30) REVERT: I 198 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7761 (mtpm) REVERT: I 272 LYS cc_start: 0.8549 (pttm) cc_final: 0.8021 (pmtt) REVERT: I 307 LYS cc_start: 0.6239 (mptt) cc_final: 0.5990 (mmtt) REVERT: R 209 VAL cc_start: 0.7723 (p) cc_final: 0.7431 (t) REVERT: R 249 ARG cc_start: 0.7502 (tpm170) cc_final: 0.7181 (tpm170) REVERT: S 174 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7993 (tp) REVERT: S 177 PHE cc_start: 0.8204 (m-10) cc_final: 0.7976 (m-80) REVERT: S 220 GLU cc_start: 0.7931 (mp0) cc_final: 0.7548 (mp0) REVERT: T 22 ARG cc_start: 0.7469 (mtt180) cc_final: 0.7149 (ttm170) REVERT: T 96 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7433 (mtt90) REVERT: T 97 SER cc_start: 0.8356 (t) cc_final: 0.8070 (p) REVERT: T 155 ASN cc_start: 0.7926 (t0) cc_final: 0.7650 (t0) REVERT: T 197 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7941 (ttp80) REVERT: T 222 PHE cc_start: 0.8562 (m-80) cc_final: 0.8350 (m-80) REVERT: T 227 SER cc_start: 0.8676 (m) cc_final: 0.8251 (m) REVERT: T 258 ASP cc_start: 0.7472 (t0) cc_final: 0.7138 (t0) REVERT: T 268 ASN cc_start: 0.7497 (t0) cc_final: 0.7247 (t0) REVERT: T 270 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (pp) outliers start: 35 outliers final: 17 residues processed: 219 average time/residue: 0.9148 time to fit residues: 216.8561 Evaluate side-chains 214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 ASP 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 190 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 30 SER 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 198 LEU 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 325 MET Chi-restraints excluded: chain T residue 333 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.0670 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN T 110 ASN T 175 GLN T 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.127901 restraints weight = 12530.900| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.16 r_work: 0.3687 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.97 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 = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8955 Z= 0.134 Angle : 0.627 13.203 12155 Z= 0.311 Chirality : 0.043 0.152 1379 Planarity : 0.004 0.040 1533 Dihedral : 6.013 51.259 1245 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.30 % Allowed : 20.79 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1104 helix: 1.91 (0.27), residues: 375 sheet: 0.08 (0.32), residues: 269 loop : -1.51 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS T 183 PHE 0.016 0.001 PHE R 230 TYR 0.013 0.001 TYR S 60 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 413) hydrogen bonds : angle 4.47506 ( 1191) SS BOND : bond 0.00686 ( 2) SS BOND : angle 1.03140 ( 4) covalent geometry : bond 0.00305 ( 8953) covalent geometry : angle 0.62723 (12151) *********************** 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 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: I 26 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: I 29 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8047 (ttmm) REVERT: I 272 LYS cc_start: 0.8549 (pttm) cc_final: 0.8038 (pmtt) REVERT: I 307 LYS cc_start: 0.6088 (mptt) cc_final: 0.5735 (mttm) REVERT: R 209 VAL cc_start: 0.7669 (p) cc_final: 0.7371 (t) REVERT: S 174 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7983 (tp) REVERT: S 220 GLU cc_start: 0.7919 (mp0) cc_final: 0.7524 (mp0) REVERT: T 22 ARG cc_start: 0.7456 (mtt180) cc_final: 0.7140 (ttm170) REVERT: T 96 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7384 (mtt90) REVERT: T 97 SER cc_start: 0.8366 (t) cc_final: 0.8041 (p) REVERT: T 212 ASP cc_start: 0.7943 (t0) cc_final: 0.7606 (t0) REVERT: T 222 PHE cc_start: 0.8617 (m-80) cc_final: 0.8381 (m-80) REVERT: T 227 SER cc_start: 0.8648 (m) cc_final: 0.8196 (m) REVERT: T 258 ASP cc_start: 0.7454 (t0) cc_final: 0.7101 (t0) REVERT: T 268 ASN cc_start: 0.7500 (t0) cc_final: 0.7245 (t0) REVERT: T 270 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8126 (pp) REVERT: T 316 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8058 (m) outliers start: 31 outliers final: 12 residues processed: 200 average time/residue: 0.9926 time to fit residues: 214.6130 Evaluate side-chains 203 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 317 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 55 optimal weight: 0.0030 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 155 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 = 0.4006 r_free = 0.4006 target = 0.144518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127262 restraints weight = 12571.870| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.18 r_work: 0.3680 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2033 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= 0.144 Angle : 0.640 17.029 12155 Z= 0.314 Chirality : 0.043 0.151 1379 Planarity : 0.004 0.043 1533 Dihedral : 5.892 50.660 1245 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.52 % Allowed : 22.39 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1104 helix: 1.96 (0.27), residues: 375 sheet: 0.11 (0.32), residues: 271 loop : -1.46 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE S 212 TYR 0.011 0.001 TYR S 190 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 413) hydrogen bonds : angle 4.42131 ( 1191) SS BOND : bond 0.00696 ( 2) SS BOND : angle 1.03893 ( 4) covalent geometry : bond 0.00332 ( 8953) covalent geometry : angle 0.63969 (12151) *********************** 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 214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8040 (ttmm) REVERT: I 33 GLU cc_start: 0.7550 (tp30) cc_final: 0.7135 (tp30) REVERT: I 43 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: I 199 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8116 (mtm) REVERT: I 307 LYS cc_start: 0.6108 (mptt) cc_final: 0.5770 (mttm) REVERT: R 209 VAL cc_start: 0.7669 (p) cc_final: 0.7368 (t) REVERT: S 174 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7969 (tp) REVERT: S 177 PHE cc_start: 0.8329 (m-10) cc_final: 0.8045 (m-80) REVERT: S 219 LEU cc_start: 0.8304 (mt) cc_final: 0.8070 (mp) REVERT: S 220 GLU cc_start: 0.7912 (mp0) cc_final: 0.7528 (mp0) REVERT: T 22 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7165 (ttm170) REVERT: T 96 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7424 (mtt90) REVERT: T 97 SER cc_start: 0.8381 (t) cc_final: 0.8076 (p) REVERT: T 222 PHE cc_start: 0.8620 (m-80) cc_final: 0.8381 (m-80) REVERT: T 227 SER cc_start: 0.8630 (m) cc_final: 0.8180 (m) REVERT: T 258 ASP cc_start: 0.7514 (t0) cc_final: 0.7140 (t0) REVERT: T 268 ASN cc_start: 0.7513 (t0) cc_final: 0.7228 (t0) REVERT: T 270 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8118 (pp) REVERT: T 316 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8039 (m) outliers start: 33 outliers final: 19 residues processed: 202 average time/residue: 0.9425 time to fit residues: 205.8962 Evaluate side-chains 201 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 199 MET 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 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 271 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 30 SER 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 198 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 175 GLN T 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.144617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127377 restraints weight = 12635.133| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.17 r_work: 0.3673 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8955 Z= 0.158 Angle : 0.653 15.971 12155 Z= 0.320 Chirality : 0.044 0.149 1379 Planarity : 0.004 0.044 1533 Dihedral : 5.858 49.594 1245 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.20 % Allowed : 23.88 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1104 helix: 2.03 (0.27), residues: 370 sheet: 0.17 (0.32), residues: 271 loop : -1.52 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE S 212 TYR 0.013 0.001 TYR S 190 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 413) hydrogen bonds : angle 4.43992 ( 1191) SS BOND : bond 0.00739 ( 2) SS BOND : angle 1.13258 ( 4) covalent geometry : bond 0.00365 ( 8953) covalent geometry : angle 0.65319 (12151) *********************** 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 220 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8051 (ttmm) REVERT: I 33 GLU cc_start: 0.7568 (tp30) cc_final: 0.7228 (tp30) REVERT: I 198 LYS cc_start: 0.8053 (mtpm) cc_final: 0.7826 (mtpm) REVERT: I 199 MET cc_start: 0.8395 (mtp) cc_final: 0.8135 (mtm) REVERT: I 307 LYS cc_start: 0.6101 (mptt) cc_final: 0.5802 (mmtm) REVERT: R 209 VAL cc_start: 0.7674 (p) cc_final: 0.7374 (t) REVERT: S 174 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7931 (tp) REVERT: S 177 PHE cc_start: 0.8310 (m-10) cc_final: 0.8017 (m-80) REVERT: S 220 GLU cc_start: 0.7890 (mp0) cc_final: 0.7505 (mp0) REVERT: T 22 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7242 (ttm170) REVERT: T 96 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7418 (mtt90) REVERT: T 97 SER cc_start: 0.8372 (t) cc_final: 0.8067 (p) REVERT: T 222 PHE cc_start: 0.8636 (m-80) cc_final: 0.8384 (m-80) REVERT: T 227 SER cc_start: 0.8624 (m) cc_final: 0.8172 (m) REVERT: T 258 ASP cc_start: 0.7543 (t0) cc_final: 0.7194 (t0) REVERT: T 268 ASN cc_start: 0.7520 (t0) cc_final: 0.7238 (t0) REVERT: T 270 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8131 (pp) REVERT: T 316 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.8003 (m) outliers start: 30 outliers final: 20 residues processed: 205 average time/residue: 1.1886 time to fit residues: 263.2988 Evaluate side-chains 212 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 30 SER 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 198 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.0270 chunk 106 optimal weight: 0.0980 overall best weight: 0.2838 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.146507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129220 restraints weight = 12761.463| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.20 r_work: 0.3702 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8955 Z= 0.116 Angle : 0.634 16.758 12155 Z= 0.308 Chirality : 0.042 0.148 1379 Planarity : 0.004 0.045 1533 Dihedral : 5.642 49.024 1245 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.67 % Allowed : 24.84 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1104 helix: 2.16 (0.27), residues: 369 sheet: 0.30 (0.33), residues: 274 loop : -1.47 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 82 HIS 0.002 0.000 HIS S 35 PHE 0.022 0.001 PHE S 212 TYR 0.009 0.001 TYR R 309 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 413) hydrogen bonds : angle 4.33210 ( 1191) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.10107 ( 4) covalent geometry : bond 0.00258 ( 8953) covalent geometry : angle 0.63362 (12151) *********************** 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 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 3.063 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8043 (ttmm) REVERT: I 33 GLU cc_start: 0.7590 (tp30) cc_final: 0.7250 (tp30) REVERT: I 43 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: I 198 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7981 (mtpm) REVERT: R 209 VAL cc_start: 0.7566 (p) cc_final: 0.7245 (t) REVERT: S 68 PHE cc_start: 0.8404 (m-10) cc_final: 0.8143 (m-10) REVERT: S 174 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7901 (tp) REVERT: S 219 LEU cc_start: 0.8282 (mt) cc_final: 0.8051 (mp) REVERT: S 220 GLU cc_start: 0.7870 (mp0) cc_final: 0.7500 (mp0) REVERT: T 22 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7179 (ttm170) REVERT: T 96 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7414 (mtt90) REVERT: T 97 SER cc_start: 0.8367 (t) cc_final: 0.8107 (p) REVERT: T 227 SER cc_start: 0.8597 (m) cc_final: 0.8156 (m) REVERT: T 258 ASP cc_start: 0.7520 (t0) cc_final: 0.7072 (t0) REVERT: T 268 ASN cc_start: 0.7492 (t0) cc_final: 0.7208 (t0) REVERT: T 270 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8107 (pp) REVERT: T 316 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7992 (m) outliers start: 25 outliers final: 16 residues processed: 198 average time/residue: 1.4181 time to fit residues: 304.1929 Evaluate side-chains 200 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU 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 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 S residue 30 SER 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 22 ARG Chi-restraints excluded: chain T residue 118 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 94 optimal weight: 0.0470 chunk 24 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128623 restraints weight = 12748.094| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.20 r_work: 0.3691 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2391 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= 0.132 Angle : 0.663 16.762 12155 Z= 0.322 Chirality : 0.043 0.144 1379 Planarity : 0.004 0.048 1533 Dihedral : 5.576 48.680 1245 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.67 % Allowed : 25.59 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1104 helix: 2.16 (0.27), residues: 369 sheet: 0.31 (0.33), residues: 270 loop : -1.41 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.001 PHE S 212 TYR 0.015 0.001 TYR S 60 ARG 0.006 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 413) hydrogen bonds : angle 4.34796 ( 1191) SS BOND : bond 0.00694 ( 2) SS BOND : angle 1.07432 ( 4) covalent geometry : bond 0.00304 ( 8953) covalent geometry : angle 0.66293 (12151) *********************** 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 203 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8029 (ttmm) REVERT: I 33 GLU cc_start: 0.7650 (tp30) cc_final: 0.7312 (tp30) REVERT: I 43 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: I 313 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8185 (mttp) REVERT: R 209 VAL cc_start: 0.7580 (p) cc_final: 0.7265 (t) REVERT: S 68 PHE cc_start: 0.8440 (m-10) cc_final: 0.8179 (m-10) REVERT: S 174 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7860 (tp) REVERT: S 219 LEU cc_start: 0.8290 (mt) cc_final: 0.8050 (mp) REVERT: S 220 GLU cc_start: 0.7853 (mp0) cc_final: 0.7483 (mp0) REVERT: T 22 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7227 (ttm170) REVERT: T 96 ARG cc_start: 0.7736 (mtt90) cc_final: 0.7379 (mtt90) REVERT: T 97 SER cc_start: 0.8361 (t) cc_final: 0.8150 (p) REVERT: T 222 PHE cc_start: 0.8597 (m-80) cc_final: 0.8329 (m-80) REVERT: T 258 ASP cc_start: 0.7471 (t0) cc_final: 0.7195 (t0) REVERT: T 268 ASN cc_start: 0.7503 (t0) cc_final: 0.7254 (t0) REVERT: T 270 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8142 (pp) REVERT: T 316 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7977 (m) outliers start: 25 outliers final: 20 residues processed: 191 average time/residue: 1.1065 time to fit residues: 226.2567 Evaluate side-chains 202 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU 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 R residue 267 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 30 SER 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 22 ARG Chi-restraints excluded: chain T residue 118 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 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 95 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.145725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128439 restraints weight = 12657.471| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.17 r_work: 0.3689 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8955 Z= 0.133 Angle : 0.657 16.392 12155 Z= 0.320 Chirality : 0.043 0.151 1379 Planarity : 0.004 0.050 1533 Dihedral : 5.507 48.957 1245 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.67 % Allowed : 25.37 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1104 helix: 2.16 (0.27), residues: 369 sheet: 0.18 (0.33), residues: 276 loop : -1.32 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.004 0.001 HIS S 35 PHE 0.025 0.001 PHE S 212 TYR 0.015 0.001 TYR S 60 ARG 0.007 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 413) hydrogen bonds : angle 4.35725 ( 1191) SS BOND : bond 0.00723 ( 2) SS BOND : angle 1.05672 ( 4) covalent geometry : bond 0.00304 ( 8953) covalent geometry : angle 0.65661 (12151) ********************** 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 203 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: I 29 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8035 (ttmm) REVERT: I 33 GLU cc_start: 0.7628 (tp30) cc_final: 0.7254 (tp30) REVERT: I 43 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: I 313 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8181 (mttp) REVERT: R 209 VAL cc_start: 0.7581 (p) cc_final: 0.7263 (t) REVERT: S 34 MET cc_start: 0.8320 (mmp) cc_final: 0.8097 (mmm) REVERT: S 68 PHE cc_start: 0.8403 (m-10) cc_final: 0.8134 (m-10) REVERT: S 174 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7872 (tp) REVERT: S 219 LEU cc_start: 0.8311 (mt) cc_final: 0.8059 (mp) REVERT: S 220 GLU cc_start: 0.7839 (mp0) cc_final: 0.7492 (mp0) REVERT: T 22 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7233 (ttm170) REVERT: T 222 PHE cc_start: 0.8601 (m-80) cc_final: 0.8345 (m-80) REVERT: T 258 ASP cc_start: 0.7482 (t0) cc_final: 0.7205 (t0) REVERT: T 268 ASN cc_start: 0.7500 (t0) cc_final: 0.7252 (t0) REVERT: T 270 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (pp) REVERT: T 316 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (m) outliers start: 25 outliers final: 21 residues processed: 190 average time/residue: 1.1032 time to fit residues: 224.4588 Evaluate side-chains 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU 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 R residue 267 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain S residue 30 SER 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 22 ARG Chi-restraints excluded: chain T residue 118 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 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 93 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 32 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.145600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.128189 restraints weight = 12772.154| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.22 r_work: 0.3688 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8955 Z= 0.133 Angle : 0.662 16.253 12155 Z= 0.322 Chirality : 0.043 0.147 1379 Planarity : 0.004 0.050 1533 Dihedral : 5.469 49.159 1245 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.67 % Allowed : 25.59 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1104 helix: 2.17 (0.27), residues: 369 sheet: 0.21 (0.32), residues: 282 loop : -1.33 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 82 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE S 212 TYR 0.014 0.001 TYR S 60 ARG 0.008 0.000 ARG T 129 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 413) hydrogen bonds : angle 4.36315 ( 1191) SS BOND : bond 0.00725 ( 2) SS BOND : angle 1.04378 ( 4) covalent geometry : bond 0.00303 ( 8953) covalent geometry : angle 0.66134 (12151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8520.38 seconds wall clock time: 149 minutes 13.73 seconds (8953.73 seconds total)