Starting phenix.real_space_refine on Thu Jul 2 12:24:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6b_25712/07_2026/7t6b_25712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6b_25712/07_2026/7t6b_25712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t6b_25712/07_2026/7t6b_25712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6b_25712/07_2026/7t6b_25712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t6b_25712/07_2026/7t6b_25712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6b_25712/07_2026/7t6b_25712.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 5571 2.51 5 N 1497 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1848 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 225, 1848 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 bond proxies already assigned to first conformer: 1874 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2038 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain breaks: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8755 At special positions: 0 Unit cell: (99.356, 121.248, 114.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 1 15.00 O 1631 8.00 N 1497 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 172 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS R 259 " - pdb=" SG CYS R 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 376.9 milliseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 33.6% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 352 through 374 removed outlier: 4.499A pdb=" N ARG A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.824A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 24 removed outlier: 4.291A pdb=" N GLN D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.508A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.952A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 21 removed outlier: 4.015A pdb=" N HIS R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR R 21 " --> pdb=" O HIS R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 61 removed outlier: 4.124A pdb=" N ALA R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 91 removed outlier: 3.513A pdb=" N PHE R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN R 74 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.826A pdb=" N THR R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER R 119 " --> pdb=" O THR R 115 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS R 136 " --> pdb=" O VAL R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 169 Proline residue: R 166 - end of helix removed outlier: 4.073A pdb=" N GLY R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 219 removed outlier: 3.567A pdb=" N SER R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 237 removed outlier: 3.709A pdb=" N LYS R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 259 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 266 through 268 No H-bonds generated for 'chain 'R' and resid 266 through 268' Processing helix chain 'R' and resid 269 through 288 removed outlier: 3.638A pdb=" N PHE R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL R 276 " --> pdb=" O TYR R 272 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER R 277 " --> pdb=" O PHE R 273 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU R 279 " --> pdb=" O ALA R 275 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER R 281 " --> pdb=" O SER R 277 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.529A pdb=" N VAL A 49 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 221 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 51 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 244 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 52 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 246 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU A 54 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N SER A 248 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 245 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASN A 291 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 247 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.564A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.687A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP C 82 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 103 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.231A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.857A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 202 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.678A pdb=" N THR C 243 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.578A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.559A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.523A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2834 1.35 - 1.48: 2215 1.48 - 1.60: 3795 1.60 - 1.73: 1 1.73 - 1.86: 78 Bond restraints: 8923 Sorted by residual: bond pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 1.677 1.858 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C1 S1P R 401 " pdb=" C2 S1P R 401 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C1 S1P R 401 " pdb=" O1 S1P R 401 " ideal model delta sigma weight residual 1.421 1.355 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C3 S1P R 401 " pdb=" O3 S1P R 401 " ideal model delta sigma weight residual 1.445 1.396 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C2 S1P R 401 " pdb=" C3 S1P R 401 " ideal model delta sigma weight residual 1.539 1.568 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 8918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 11772 2.04 - 4.09: 264 4.09 - 6.13: 38 6.13 - 8.17: 6 8.17 - 10.22: 3 Bond angle restraints: 12083 Sorted by residual: angle pdb=" N VAL A 302 " pdb=" CA VAL A 302 " pdb=" C VAL A 302 " ideal model delta sigma weight residual 113.53 110.61 2.92 9.80e-01 1.04e+00 8.87e+00 angle pdb=" CA GLY C 115 " pdb=" C GLY C 115 " pdb=" N GLY C 116 " ideal model delta sigma weight residual 114.58 117.09 -2.51 8.60e-01 1.35e+00 8.55e+00 angle pdb=" CA LEU A 54 " pdb=" CB LEU A 54 " pdb=" CG LEU A 54 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 angle pdb=" N SER C 275 " pdb=" CA SER C 275 " pdb=" C SER C 275 " ideal model delta sigma weight residual 108.32 112.94 -4.62 1.64e+00 3.72e-01 7.93e+00 angle pdb=" C4 S1P R 401 " pdb=" C3 S1P R 401 " pdb=" O3 S1P R 401 " ideal model delta sigma weight residual 110.00 101.59 8.41 3.00e+00 1.11e-01 7.86e+00 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 5208 35.39 - 70.78: 104 70.78 - 106.17: 9 106.17 - 141.57: 1 141.57 - 176.96: 3 Dihedral angle restraints: 5325 sinusoidal: 2082 harmonic: 3243 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CA VAL R 238 " pdb=" C VAL R 238 " pdb=" N LEU R 239 " pdb=" CA LEU R 239 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA A 349 " pdb=" C ALA A 349 " pdb=" N ILE A 350 " pdb=" CA ILE A 350 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1218 0.070 - 0.139: 169 0.139 - 0.209: 9 0.209 - 0.278: 0 0.278 - 0.348: 1 Chirality restraints: 1397 Sorted by residual: chirality pdb=" C2 S1P R 401 " pdb=" C1 S1P R 401 " pdb=" C3 S1P R 401 " pdb=" N2 S1P R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.77 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA PRO E 41 " pdb=" N PRO E 41 " pdb=" C PRO E 41 " pdb=" CB PRO E 41 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1394 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 49 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 236 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 165 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO R 166 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.029 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 658 2.74 - 3.28: 8441 3.28 - 3.82: 13677 3.82 - 4.36: 16649 4.36 - 4.90: 29386 Nonbonded interactions: 68811 Sorted by model distance: nonbonded pdb=" O THR R 278 " pdb=" OG SER R 281 " model vdw 2.195 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.245 3.040 nonbonded pdb=" O LEU R 162 " pdb=" OH TYR R 190 " model vdw 2.254 3.040 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.258 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.296 3.040 ... (remaining 68806 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: 1.470 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.005 0.181 8927 Z= 0.216 Angle : 0.768 10.217 12091 Z= 0.415 Chirality : 0.048 0.348 1397 Planarity : 0.005 0.054 1519 Dihedral : 15.843 176.956 3217 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.21 % Allowed : 4.47 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.21), residues: 1099 helix: -1.34 (0.24), residues: 362 sheet: -2.95 (0.27), residues: 277 loop : -3.16 (0.23), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 47 TYR 0.016 0.002 TYR C 59 PHE 0.018 0.002 PHE A 234 TRP 0.023 0.002 TRP C 211 HIS 0.007 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 ( 8923) covalent geometry : angle 0.76827 / 0.41 (12083) SS BOND : bond 0.00310 / 0.15 ( 4) SS BOND : angle 0.93752 / 0.50 ( 8) hydrogen bonds : bond 0.14698 / 9.82 ( 378) hydrogen bonds : angle 6.37139 / 4.37 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.5998 (pmt-80) cc_final: 0.5368 (pmt-80) REVERT: A 340 LYS cc_start: 0.7121 (ptmt) cc_final: 0.6253 (mmmt) REVERT: A 369 ASP cc_start: 0.8047 (t0) cc_final: 0.7473 (t0) REVERT: C 42 ARG cc_start: 0.7710 (tpt-90) cc_final: 0.7499 (tpt170) REVERT: C 46 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.6891 (mtp85) REVERT: C 204 CYS cc_start: 0.7246 (t) cc_final: 0.6588 (t) REVERT: D 62 ARG cc_start: 0.6013 (tpm170) cc_final: 0.5685 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.0835 time to fit residues: 14.6743 Evaluate side-chains 100 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 GLN C 6 GLN C 91 HIS C 259 GLN C 340 ASN E 13 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.189710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119071 restraints weight = 9071.862| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.42 r_work: 0.3120 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8927 Z= 0.140 Angle : 0.580 9.735 12091 Z= 0.303 Chirality : 0.042 0.149 1397 Planarity : 0.004 0.046 1519 Dihedral : 11.605 174.035 1232 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.04 % Allowed : 10.20 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.24), residues: 1099 helix: 0.08 (0.26), residues: 372 sheet: -2.53 (0.28), residues: 285 loop : -2.66 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.017 0.001 TYR E 190 PHE 0.012 0.001 PHE A 234 TRP 0.016 0.001 TRP C 211 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 8923) covalent geometry : angle 0.57975 / 0.30 (12083) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 1.00164 / 0.54 ( 8) hydrogen bonds : bond 0.03844 / 2.60 ( 378) hydrogen bonds : angle 4.56766 / 3.15 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7092 (ptmt) cc_final: 0.5897 (mmmt) REVERT: C 46 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.6439 (mtp85) REVERT: C 59 TYR cc_start: 0.8807 (m-80) cc_final: 0.8314 (m-80) REVERT: C 204 CYS cc_start: 0.8071 (t) cc_final: 0.7753 (t) REVERT: D 52 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.6984 (p) REVERT: D 62 ARG cc_start: 0.6358 (tpm170) cc_final: 0.5228 (ttp80) REVERT: E 113 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7758 (mm-40) REVERT: E 202 ARG cc_start: 0.7084 (mtm-85) cc_final: 0.6866 (mtp-110) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.0845 time to fit residues: 12.0380 Evaluate side-chains 98 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.191061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119167 restraints weight = 8903.765| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.45 r_work: 0.3148 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8927 Z= 0.134 Angle : 0.547 10.372 12091 Z= 0.287 Chirality : 0.041 0.142 1397 Planarity : 0.004 0.045 1519 Dihedral : 11.006 163.655 1232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.77 % Allowed : 11.76 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.25), residues: 1099 helix: 0.74 (0.28), residues: 372 sheet: -2.16 (0.28), residues: 295 loop : -2.33 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.016 0.001 TYR E 190 PHE 0.012 0.001 PHE C 241 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8923) covalent geometry : angle 0.54698 / 0.29 (12083) SS BOND : bond 0.00276 / 0.13 ( 4) SS BOND : angle 0.98926 / 0.52 ( 8) hydrogen bonds : bond 0.03564 / 2.42 ( 378) hydrogen bonds : angle 4.23064 / 2.93 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6038 (mmmt) REVERT: C 46 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.6529 (mtp85) REVERT: C 59 TYR cc_start: 0.8899 (m-80) cc_final: 0.8463 (m-80) REVERT: C 153 ASP cc_start: 0.7515 (m-30) cc_final: 0.7251 (m-30) REVERT: C 170 ASP cc_start: 0.7839 (t70) cc_final: 0.7455 (t0) REVERT: C 204 CYS cc_start: 0.8192 (t) cc_final: 0.7892 (t) REVERT: D 52 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7168 (p) REVERT: D 62 ARG cc_start: 0.6460 (tpm170) cc_final: 0.5396 (ttp80) REVERT: E 113 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7895 (mm-40) REVERT: E 202 ARG cc_start: 0.7195 (mtm-85) cc_final: 0.6988 (mtp-110) REVERT: R 268 TYR cc_start: 0.8021 (m-80) cc_final: 0.7632 (m-80) REVERT: R 272 TYR cc_start: 0.8039 (m-80) cc_final: 0.7510 (m-80) REVERT: R 281 SER cc_start: 0.8133 (t) cc_final: 0.7799 (p) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 0.0818 time to fit residues: 13.3141 Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.192776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116891 restraints weight = 9198.731| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.28 r_work: 0.3102 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8927 Z= 0.108 Angle : 0.507 10.333 12091 Z= 0.267 Chirality : 0.040 0.135 1397 Planarity : 0.003 0.044 1519 Dihedral : 10.535 157.777 1232 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.08 % Allowed : 13.53 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.25), residues: 1099 helix: 1.15 (0.28), residues: 372 sheet: -1.91 (0.28), residues: 295 loop : -2.07 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.014 0.001 TYR E 190 PHE 0.010 0.001 PHE C 241 TRP 0.010 0.001 TRP C 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8923) covalent geometry : angle 0.50692 / 0.27 (12083) SS BOND : bond 0.00247 / 0.12 ( 4) SS BOND : angle 0.84374 / 0.44 ( 8) hydrogen bonds : bond 0.03247 / 2.21 ( 378) hydrogen bonds : angle 4.01813 / 2.79 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.232 Fit side-chains REVERT: A 340 LYS cc_start: 0.7109 (ptmt) cc_final: 0.6013 (mmmt) REVERT: C 46 ARG cc_start: 0.7511 (ttt-90) cc_final: 0.6374 (mtp85) REVERT: C 59 TYR cc_start: 0.8821 (m-80) cc_final: 0.8501 (m-80) REVERT: C 153 ASP cc_start: 0.7331 (m-30) cc_final: 0.7113 (m-30) REVERT: C 170 ASP cc_start: 0.7742 (t70) cc_final: 0.7374 (t0) REVERT: C 204 CYS cc_start: 0.8058 (t) cc_final: 0.7689 (t) REVERT: C 234 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: D 52 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7228 (p) REVERT: D 62 ARG cc_start: 0.6266 (tpm170) cc_final: 0.5323 (ttp80) REVERT: R 268 TYR cc_start: 0.8012 (m-80) cc_final: 0.7687 (m-80) REVERT: R 272 TYR cc_start: 0.7944 (m-80) cc_final: 0.7424 (m-80) outliers start: 20 outliers final: 8 residues processed: 127 average time/residue: 0.0777 time to fit residues: 13.5620 Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.185904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109335 restraints weight = 9161.918| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.81 r_work: 0.2983 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8927 Z= 0.212 Angle : 0.603 10.085 12091 Z= 0.315 Chirality : 0.043 0.145 1397 Planarity : 0.004 0.047 1519 Dihedral : 10.814 164.564 1232 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.50 % Allowed : 16.02 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.25), residues: 1099 helix: 1.17 (0.28), residues: 372 sheet: -1.92 (0.28), residues: 292 loop : -2.03 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.024 0.002 TYR E 175 PHE 0.015 0.002 PHE C 241 TRP 0.013 0.002 TRP C 211 HIS 0.009 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 ( 8923) covalent geometry : angle 0.60287 / 0.32 (12083) SS BOND : bond 0.00409 / 0.20 ( 4) SS BOND : angle 1.21565 / 0.63 ( 8) hydrogen bonds : bond 0.04060 / 2.75 ( 378) hydrogen bonds : angle 4.19543 / 2.91 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.333 Fit side-chains REVERT: A 320 ARG cc_start: 0.7333 (mtp180) cc_final: 0.7071 (mtp180) REVERT: A 340 LYS cc_start: 0.7211 (ptmt) cc_final: 0.6032 (mmmt) REVERT: C 46 ARG cc_start: 0.7407 (ttt-90) cc_final: 0.6325 (mtp85) REVERT: C 59 TYR cc_start: 0.8865 (m-80) cc_final: 0.8218 (m-80) REVERT: C 153 ASP cc_start: 0.7628 (m-30) cc_final: 0.7372 (m-30) REVERT: C 204 CYS cc_start: 0.8183 (t) cc_final: 0.7890 (t) REVERT: C 234 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: D 62 ARG cc_start: 0.6551 (tpm170) cc_final: 0.5281 (ttp80) REVERT: R 268 TYR cc_start: 0.7974 (m-80) cc_final: 0.7677 (m-80) REVERT: R 272 TYR cc_start: 0.8057 (m-80) cc_final: 0.7416 (m-80) outliers start: 24 outliers final: 11 residues processed: 122 average time/residue: 0.0794 time to fit residues: 13.5729 Evaluate side-chains 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 2 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.192706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121109 restraints weight = 9092.548| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.44 r_work: 0.3149 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8927 Z= 0.106 Angle : 0.516 10.061 12091 Z= 0.268 Chirality : 0.041 0.140 1397 Planarity : 0.003 0.041 1519 Dihedral : 10.583 176.681 1232 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.77 % Allowed : 17.59 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.26), residues: 1099 helix: 1.44 (0.28), residues: 372 sheet: -1.55 (0.29), residues: 279 loop : -1.92 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.016 0.001 TYR R 213 PHE 0.011 0.001 PHE C 292 TRP 0.008 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8923) covalent geometry : angle 0.51592 / 0.27 (12083) SS BOND : bond 0.00255 / 0.12 ( 4) SS BOND : angle 0.70101 / 0.36 ( 8) hydrogen bonds : bond 0.03198 / 2.18 ( 378) hydrogen bonds : angle 3.94664 / 2.75 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: C 46 ARG cc_start: 0.7485 (ttt-90) cc_final: 0.6313 (mtp85) REVERT: C 59 TYR cc_start: 0.8859 (m-80) cc_final: 0.8368 (m-80) REVERT: C 152 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7633 (tt) REVERT: C 153 ASP cc_start: 0.7110 (m-30) cc_final: 0.6840 (m-30) REVERT: C 170 ASP cc_start: 0.7591 (t70) cc_final: 0.7231 (t0) REVERT: C 204 CYS cc_start: 0.8140 (t) cc_final: 0.7845 (t) REVERT: C 234 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: D 62 ARG cc_start: 0.6326 (tpm170) cc_final: 0.5235 (ttp80) REVERT: E 202 ARG cc_start: 0.6811 (mtp-110) cc_final: 0.6367 (ttp80) REVERT: R 268 TYR cc_start: 0.7970 (m-80) cc_final: 0.7707 (m-80) REVERT: R 287 ILE cc_start: 0.6628 (mm) cc_final: 0.6407 (mm) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.0861 time to fit residues: 13.7336 Evaluate side-chains 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.192348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121065 restraints weight = 9057.762| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.43 r_work: 0.3149 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8927 Z= 0.109 Angle : 0.512 10.191 12091 Z= 0.267 Chirality : 0.040 0.132 1397 Planarity : 0.003 0.041 1519 Dihedral : 10.210 177.711 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.29 % Allowed : 17.27 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.26), residues: 1099 helix: 1.41 (0.28), residues: 380 sheet: -1.35 (0.30), residues: 278 loop : -1.74 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.019 0.001 TYR R 213 PHE 0.013 0.001 PHE C 292 TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8923) covalent geometry : angle 0.51157 / 0.27 (12083) SS BOND : bond 0.00252 / 0.12 ( 4) SS BOND : angle 0.74640 / 0.39 ( 8) hydrogen bonds : bond 0.03203 / 2.19 ( 378) hydrogen bonds : angle 3.87951 / 2.70 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.312 Fit side-chains REVERT: A 334 ARG cc_start: 0.5998 (mtm180) cc_final: 0.5736 (ttp80) REVERT: A 340 LYS cc_start: 0.7050 (ptmt) cc_final: 0.5961 (mmmt) REVERT: C 46 ARG cc_start: 0.7483 (ttt-90) cc_final: 0.6297 (mtp85) REVERT: C 59 TYR cc_start: 0.8835 (m-80) cc_final: 0.8352 (m-80) REVERT: C 153 ASP cc_start: 0.7278 (m-30) cc_final: 0.7025 (m-30) REVERT: C 170 ASP cc_start: 0.7568 (t70) cc_final: 0.7208 (t0) REVERT: C 204 CYS cc_start: 0.8163 (t) cc_final: 0.7840 (t) REVERT: C 234 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: D 62 ARG cc_start: 0.6249 (tpm170) cc_final: 0.5154 (ttp80) REVERT: E 202 ARG cc_start: 0.6915 (mtp-110) cc_final: 0.6281 (ttp80) REVERT: R 281 SER cc_start: 0.7800 (t) cc_final: 0.7537 (p) REVERT: R 283 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7227 (mp) REVERT: R 287 ILE cc_start: 0.6604 (mm) cc_final: 0.6392 (mm) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.0858 time to fit residues: 14.0690 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 90 optimal weight: 0.0000 chunk 84 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.195837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126752 restraints weight = 9032.251| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.78 r_work: 0.3188 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8927 Z= 0.089 Angle : 0.490 10.138 12091 Z= 0.255 Chirality : 0.040 0.132 1397 Planarity : 0.003 0.035 1519 Dihedral : 9.499 175.805 1232 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.66 % Allowed : 17.90 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.26), residues: 1099 helix: 1.59 (0.28), residues: 379 sheet: -1.22 (0.29), residues: 290 loop : -1.65 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.017 0.001 TYR R 213 PHE 0.012 0.001 PHE C 292 TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 ( 8923) covalent geometry : angle 0.49016 / 0.26 (12083) SS BOND : bond 0.00271 / 0.13 ( 4) SS BOND : angle 0.62098 / 0.32 ( 8) hydrogen bonds : bond 0.02881 / 1.96 ( 378) hydrogen bonds : angle 3.75625 / 2.63 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.318 Fit side-chains REVERT: A 20 ASP cc_start: 0.8077 (m-30) cc_final: 0.7828 (m-30) REVERT: A 340 LYS cc_start: 0.6928 (ptmt) cc_final: 0.5779 (mmmt) REVERT: C 46 ARG cc_start: 0.7555 (ttt-90) cc_final: 0.6284 (mtp85) REVERT: C 59 TYR cc_start: 0.8824 (m-80) cc_final: 0.8394 (m-80) REVERT: C 130 GLU cc_start: 0.8248 (mp0) cc_final: 0.8029 (mp0) REVERT: C 152 LEU cc_start: 0.7889 (tt) cc_final: 0.7635 (tt) REVERT: C 153 ASP cc_start: 0.7052 (m-30) cc_final: 0.6752 (m-30) REVERT: C 170 ASP cc_start: 0.7542 (t70) cc_final: 0.7179 (t0) REVERT: C 204 CYS cc_start: 0.8058 (t) cc_final: 0.7753 (t) REVERT: C 234 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: D 62 ARG cc_start: 0.6196 (tpm170) cc_final: 0.5191 (ttp80) REVERT: E 202 ARG cc_start: 0.6965 (mtp-110) cc_final: 0.6349 (ttp80) REVERT: R 281 SER cc_start: 0.7735 (t) cc_final: 0.7461 (p) REVERT: R 283 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7208 (mp) REVERT: R 287 ILE cc_start: 0.6508 (mm) cc_final: 0.6307 (mm) outliers start: 16 outliers final: 10 residues processed: 113 average time/residue: 0.0875 time to fit residues: 13.4935 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 283 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 90 optimal weight: 0.0770 chunk 28 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.195767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127024 restraints weight = 8995.320| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.58 r_work: 0.3189 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8927 Z= 0.092 Angle : 0.495 12.522 12091 Z= 0.256 Chirality : 0.040 0.129 1397 Planarity : 0.003 0.038 1519 Dihedral : 8.854 173.719 1232 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.87 % Allowed : 18.00 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.26), residues: 1099 helix: 1.67 (0.28), residues: 379 sheet: -1.03 (0.30), residues: 277 loop : -1.65 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.015 0.001 TYR R 213 PHE 0.014 0.001 PHE C 292 TRP 0.008 0.001 TRP A 233 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 8923) covalent geometry : angle 0.49501 / 0.26 (12083) SS BOND : bond 0.00267 / 0.13 ( 4) SS BOND : angle 0.67540 / 0.34 ( 8) hydrogen bonds : bond 0.02951 / 2.01 ( 378) hydrogen bonds : angle 3.70370 / 2.61 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.267 Fit side-chains REVERT: A 20 ASP cc_start: 0.8068 (m-30) cc_final: 0.7835 (m-30) REVERT: A 340 LYS cc_start: 0.6898 (ptmt) cc_final: 0.5700 (mmmt) REVERT: C 46 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.6296 (mtp85) REVERT: C 59 TYR cc_start: 0.8823 (m-80) cc_final: 0.8442 (m-80) REVERT: C 130 GLU cc_start: 0.8257 (mp0) cc_final: 0.8043 (mp0) REVERT: C 152 LEU cc_start: 0.7935 (tt) cc_final: 0.7670 (tt) REVERT: C 153 ASP cc_start: 0.7166 (m-30) cc_final: 0.6887 (m-30) REVERT: C 170 ASP cc_start: 0.7540 (t70) cc_final: 0.7169 (t0) REVERT: C 204 CYS cc_start: 0.8057 (t) cc_final: 0.7783 (t) REVERT: C 234 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: D 62 ARG cc_start: 0.6165 (tpm170) cc_final: 0.5159 (ttp80) REVERT: E 202 ARG cc_start: 0.6994 (mtp-110) cc_final: 0.6378 (ttp80) REVERT: R 281 SER cc_start: 0.7671 (t) cc_final: 0.7394 (p) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.0809 time to fit residues: 13.0633 Evaluate side-chains 117 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.193898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124301 restraints weight = 8998.963| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.61 r_work: 0.3164 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8927 Z= 0.114 Angle : 0.528 12.171 12091 Z= 0.273 Chirality : 0.041 0.206 1397 Planarity : 0.003 0.039 1519 Dihedral : 8.474 174.685 1232 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.46 % Allowed : 18.00 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.26), residues: 1099 helix: 1.73 (0.28), residues: 379 sheet: -1.10 (0.30), residues: 280 loop : -1.61 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.015 0.001 TYR E 190 PHE 0.015 0.001 PHE C 292 TRP 0.007 0.001 TRP A 233 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8923) covalent geometry : angle 0.52801 / 0.27 (12083) SS BOND : bond 0.00300 / 0.14 ( 4) SS BOND : angle 0.73593 / 0.37 ( 8) hydrogen bonds : bond 0.03129 / 2.13 ( 378) hydrogen bonds : angle 3.74698 / 2.63 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.244 Fit side-chains REVERT: C 46 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.6281 (mtp85) REVERT: C 59 TYR cc_start: 0.8851 (m-80) cc_final: 0.8558 (m-80) REVERT: C 61 MET cc_start: 0.8922 (ppp) cc_final: 0.8615 (ppp) REVERT: C 130 GLU cc_start: 0.8315 (mp0) cc_final: 0.8106 (mp0) REVERT: C 153 ASP cc_start: 0.7238 (m-30) cc_final: 0.6981 (m-30) REVERT: C 170 ASP cc_start: 0.7577 (t70) cc_final: 0.7203 (t0) REVERT: C 204 CYS cc_start: 0.8077 (t) cc_final: 0.7813 (t) REVERT: C 234 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: C 262 MET cc_start: 0.8428 (ttm) cc_final: 0.7926 (mmm) REVERT: D 62 ARG cc_start: 0.6166 (tpm170) cc_final: 0.5091 (ttp80) REVERT: E 202 ARG cc_start: 0.6975 (mtp-110) cc_final: 0.6316 (ttp80) REVERT: R 281 SER cc_start: 0.7687 (t) cc_final: 0.7444 (p) outliers start: 14 outliers final: 12 residues processed: 113 average time/residue: 0.0727 time to fit residues: 11.5229 Evaluate side-chains 115 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.193917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124598 restraints weight = 8936.057| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.57 r_work: 0.3163 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8927 Z= 0.110 Angle : 0.519 12.159 12091 Z= 0.269 Chirality : 0.041 0.195 1397 Planarity : 0.003 0.039 1519 Dihedral : 7.458 178.702 1232 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.46 % Allowed : 18.63 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.26), residues: 1099 helix: 1.79 (0.28), residues: 379 sheet: -0.91 (0.31), residues: 268 loop : -1.66 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.014 0.001 TYR R 213 PHE 0.013 0.001 PHE C 292 TRP 0.007 0.001 TRP A 233 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8923) covalent geometry : angle 0.51897 / 0.27 (12083) SS BOND : bond 0.00297 / 0.14 ( 4) SS BOND : angle 0.71754 / 0.36 ( 8) hydrogen bonds : bond 0.03104 / 2.11 ( 378) hydrogen bonds : angle 3.72994 / 2.62 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.76 seconds wall clock time: 44 minutes 16.75 seconds (2656.75 seconds total)