Starting phenix.real_space_refine on Thu Jul 2 09:49:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f58_31461/07_2026/7f58_31461.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 Cl 1 4.86 5 C 5112 2.51 5 N 1389 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 8065 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 49 Unusual residues: {' CA': 1, '1I8': 1} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.21 Number of scatterers: 8065 At special positions: 0 Unit cell: (86.19, 96.33, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 62 16.00 O 1500 8.00 N 1389 7.00 C 5112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.76 Conformation dependent library (CDL) restraints added in 510.7 milliseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 44.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.974A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 removed outlier: 4.007A pdb=" N THR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 153 removed outlier: 4.051A pdb=" N ASN R 123 " --> pdb=" O VAL R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 190 through 228 removed outlier: 3.586A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET R 200 " --> pdb=" O CYS R 196 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.813A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 Processing helix chain 'R' and resid 283 through 302 removed outlier: 3.528A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 306 through 320 Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.943A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.696A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.978A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.705A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.447A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.877A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.247A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.129A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.573A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.907A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.537A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.651A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.283A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.508A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.739A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.503A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1245 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: 1.20 Time building geometry restraints manager: 0.99 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: 1313 1.31 - 1.44: 2213 1.44 - 1.57: 4594 1.57 - 1.70: 5 1.70 - 1.82: 88 Bond restraints: 8213 Sorted by residual: bond pdb=" C33 1I8 R 601 " pdb=" C38 1I8 R 601 " ideal model delta sigma weight residual 1.388 1.572 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C28 1I8 R 601 " pdb=" N07 1I8 R 601 " ideal model delta sigma weight residual 1.337 1.512 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C35 1I8 R 601 " pdb=" C39 1I8 R 601 " ideal model delta sigma weight residual 1.387 1.562 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" C39 1I8 R 601 " pdb=" C42 1I8 R 601 " ideal model delta sigma weight residual 1.390 1.564 -0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C31 1I8 R 601 " pdb=" C36 1I8 R 601 " ideal model delta sigma weight residual 1.386 1.549 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 8208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10811 1.99 - 3.98: 261 3.98 - 5.97: 34 5.97 - 7.96: 11 7.96 - 9.96: 3 Bond angle restraints: 11120 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 111.28 121.24 -9.96 1.09e+00 8.42e-01 8.34e+01 angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.13 116.75 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" N VAL B 315 " pdb=" CA VAL B 315 " pdb=" C VAL B 315 " ideal model delta sigma weight residual 106.21 111.01 -4.80 1.07e+00 8.73e-01 2.01e+01 angle pdb=" CA PRO R 299 " pdb=" N PRO R 299 " pdb=" CD PRO R 299 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.92e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 118.74 -5.21 1.39e+00 5.18e-01 1.41e+01 ... (remaining 11115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4534 17.61 - 35.21: 289 35.21 - 52.82: 63 52.82 - 70.42: 16 70.42 - 88.03: 9 Dihedral angle restraints: 4911 sinusoidal: 1939 harmonic: 2972 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -13.19 -72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -40.19 -45.81 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CG ARG A 13 " pdb=" CD ARG A 13 " pdb=" NE ARG A 13 " pdb=" CZ ARG A 13 " ideal model delta sinusoidal sigma weight residual 180.00 135.78 44.22 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 4908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1008 0.056 - 0.112: 219 0.112 - 0.168: 37 0.168 - 0.225: 5 0.225 - 0.281: 2 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CB ILE R 194 " pdb=" CA ILE R 194 " pdb=" CG1 ILE R 194 " pdb=" CG2 ILE R 194 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA SER B 316 " pdb=" N SER B 316 " pdb=" C SER B 316 " pdb=" CB SER B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1268 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 298 " -0.096 5.00e-02 4.00e+02 1.43e-01 3.28e+01 pdb=" N PRO R 299 " 0.248 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 374 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ARG A 374 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG A 374 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 375 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 126 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C ASP R 126 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP R 126 " 0.019 2.00e-02 2.50e+03 pdb=" N SER R 127 " 0.017 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2161 2.80 - 3.33: 7736 3.33 - 3.85: 13691 3.85 - 4.38: 16483 4.38 - 4.90: 28030 Nonbonded interactions: 68101 Sorted by model distance: nonbonded pdb=" NH1 ARG R 305 " pdb=" OE2 GLU A 392 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.299 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.301 3.120 nonbonded pdb=" OE1 GLN A 236 " pdb=" NH1 ARG B 314 " model vdw 2.310 3.120 ... (remaining 68096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.008 0.184 8217 Z= 0.392 Angle : 0.791 9.956 11128 Z= 0.467 Chirality : 0.049 0.281 1271 Planarity : 0.006 0.143 1410 Dihedral : 12.918 88.029 2973 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 0.23 % Allowed : 4.09 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1001 helix: 0.84 (0.24), residues: 405 sheet: 0.88 (0.36), residues: 211 loop : 0.35 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 72 TYR 0.020 0.002 TYR A 339 PHE 0.021 0.002 PHE R 262 TRP 0.024 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.39 ( 8213) covalent geometry : angle 0.78963 / 0.47 (11120) SS BOND : bond 0.00223 / 0.15 ( 4) SS BOND : angle 2.00527 / 1.00 ( 8) hydrogen bonds : bond 0.14286 / 9.69 ( 441) hydrogen bonds : angle 6.16111 / 4.49 ( 1245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: R 215 MET cc_start: 0.8367 (mtp) cc_final: 0.8129 (mtm) REVERT: R 220 ARG cc_start: 0.7075 (ttp80) cc_final: 0.6754 (ttp-170) REVERT: R 309 LEU cc_start: 0.7564 (mt) cc_final: 0.7269 (tt) REVERT: B 61 MET cc_start: 0.7152 (tmm) cc_final: 0.6904 (ttp) REVERT: B 186 ASP cc_start: 0.7380 (m-30) cc_final: 0.7040 (m-30) REVERT: B 325 MET cc_start: 0.7518 (mmm) cc_final: 0.7179 (mmt) REVERT: N 108 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5738 (m-80) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.1179 time to fit residues: 31.8245 Evaluate side-chains 157 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 294 ASN A 357 HIS B 9 GLN B 16 ASN B 32 GLN B 132 ASN B 176 GLN B 259 GLN N 3 GLN N 13 GLN N 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.169574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132435 restraints weight = 8700.822| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.70 r_work: 0.3301 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8217 Z= 0.189 Angle : 0.592 7.577 11128 Z= 0.322 Chirality : 0.044 0.168 1271 Planarity : 0.005 0.080 1410 Dihedral : 4.995 36.768 1126 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.82 % Allowed : 7.95 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1001 helix: 1.88 (0.24), residues: 409 sheet: 0.62 (0.33), residues: 237 loop : 0.44 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.021 0.001 TYR A 339 PHE 0.021 0.002 PHE N 108 TRP 0.019 0.002 TRP B 211 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 8213) covalent geometry : angle 0.59101 / 0.32 (11120) SS BOND : bond 0.00214 / 0.11 ( 4) SS BOND : angle 1.23101 / 0.66 ( 8) hydrogen bonds : bond 0.04828 / 3.30 ( 441) hydrogen bonds : angle 4.76180 / 3.43 ( 1245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: R 215 MET cc_start: 0.8611 (mtp) cc_final: 0.8398 (mtm) REVERT: R 220 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7470 (ttm-80) REVERT: A 343 ASP cc_start: 0.8356 (m-30) cc_final: 0.8044 (m-30) REVERT: B 97 SER cc_start: 0.8456 (p) cc_final: 0.8021 (m) REVERT: B 186 ASP cc_start: 0.7856 (m-30) cc_final: 0.7654 (m-30) REVERT: B 226 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 254 ASP cc_start: 0.8517 (p0) cc_final: 0.7747 (t0) REVERT: N 5 GLN cc_start: 0.7564 (mp10) cc_final: 0.7341 (mp10) outliers start: 16 outliers final: 10 residues processed: 171 average time/residue: 0.1078 time to fit residues: 24.4640 Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136462 restraints weight = 8621.890| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.73 r_work: 0.3357 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8217 Z= 0.115 Angle : 0.492 7.739 11128 Z= 0.267 Chirality : 0.041 0.160 1271 Planarity : 0.004 0.063 1410 Dihedral : 4.581 35.340 1124 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.59 % Allowed : 9.55 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1001 helix: 2.32 (0.24), residues: 410 sheet: 0.73 (0.34), residues: 219 loop : 0.35 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.013 0.001 TYR A 339 PHE 0.013 0.001 PHE R 262 TRP 0.018 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 8213) covalent geometry : angle 0.49211 / 0.27 (11120) SS BOND : bond 0.00215 / 0.12 ( 4) SS BOND : angle 0.84291 / 0.48 ( 8) hydrogen bonds : bond 0.03973 / 2.68 ( 441) hydrogen bonds : angle 4.36982 / 3.15 ( 1245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7373 (ttm-80) REVERT: A 343 ASP cc_start: 0.8268 (m-30) cc_final: 0.7972 (m-30) REVERT: A 356 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7946 (mtm110) REVERT: B 59 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8350 (t80) REVERT: B 226 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 254 ASP cc_start: 0.8551 (p0) cc_final: 0.7739 (t0) REVERT: N 5 GLN cc_start: 0.7561 (mp10) cc_final: 0.7089 (mp10) outliers start: 14 outliers final: 9 residues processed: 164 average time/residue: 0.1008 time to fit residues: 22.2028 Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 294 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136513 restraints weight = 8747.435| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.68 r_work: 0.3359 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8217 Z= 0.111 Angle : 0.470 6.508 11128 Z= 0.255 Chirality : 0.040 0.145 1271 Planarity : 0.004 0.057 1410 Dihedral : 4.458 34.745 1124 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.05 % Allowed : 11.25 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1001 helix: 2.39 (0.24), residues: 414 sheet: 0.61 (0.34), residues: 219 loop : 0.32 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.013 0.001 TYR A 339 PHE 0.012 0.001 PHE N 108 TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 8213) covalent geometry : angle 0.46967 / 0.26 (11120) SS BOND : bond 0.00192 / 0.11 ( 4) SS BOND : angle 0.73969 / 0.44 ( 8) hydrogen bonds : bond 0.03742 / 2.54 ( 441) hydrogen bonds : angle 4.20410 / 3.02 ( 1245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5272 (mm) REVERT: R 200 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6809 (ptp) REVERT: A 356 ARG cc_start: 0.8270 (mtm110) cc_final: 0.8006 (mtm110) REVERT: B 226 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7759 (mt-10) REVERT: N 5 GLN cc_start: 0.7626 (mp10) cc_final: 0.7179 (mp10) outliers start: 18 outliers final: 13 residues processed: 175 average time/residue: 0.1063 time to fit residues: 24.6751 Evaluate side-chains 165 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 200 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 31 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.178748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143716 restraints weight = 8485.353| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.65 r_work: 0.3330 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8217 Z= 0.123 Angle : 0.470 5.926 11128 Z= 0.257 Chirality : 0.041 0.150 1271 Planarity : 0.004 0.052 1410 Dihedral : 4.442 34.318 1124 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 11.36 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 1001 helix: 2.42 (0.24), residues: 414 sheet: 0.47 (0.33), residues: 231 loop : 0.36 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.014 0.001 TYR A 339 PHE 0.016 0.001 PHE N 108 TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8213) covalent geometry : angle 0.47008 / 0.26 (11120) SS BOND : bond 0.00223 / 0.13 ( 4) SS BOND : angle 0.78948 / 0.49 ( 8) hydrogen bonds : bond 0.03772 / 2.56 ( 441) hydrogen bonds : angle 4.16312 / 2.99 ( 1245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5196 (mm) REVERT: A 356 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7972 (mtm110) REVERT: B 254 ASP cc_start: 0.8545 (p0) cc_final: 0.7719 (t0) REVERT: N 5 GLN cc_start: 0.7633 (mp10) cc_final: 0.7391 (mp10) outliers start: 19 outliers final: 15 residues processed: 161 average time/residue: 0.0995 time to fit residues: 21.6581 Evaluate side-chains 163 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.0060 chunk 6 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 31 GLN A 371 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135505 restraints weight = 8668.240| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.73 r_work: 0.3355 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8217 Z= 0.107 Angle : 0.454 6.103 11128 Z= 0.246 Chirality : 0.040 0.143 1271 Planarity : 0.004 0.050 1410 Dihedral : 4.360 34.224 1124 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.50 % Allowed : 11.93 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.27), residues: 1001 helix: 2.43 (0.25), residues: 420 sheet: 0.39 (0.33), residues: 226 loop : 0.32 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.013 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.018 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 8213) covalent geometry : angle 0.45329 / 0.25 (11120) SS BOND : bond 0.00218 / 0.13 ( 4) SS BOND : angle 0.72246 / 0.46 ( 8) hydrogen bonds : bond 0.03596 / 2.43 ( 441) hydrogen bonds : angle 4.07392 / 2.92 ( 1245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5000 (mm) REVERT: R 161 MET cc_start: 0.7322 (mmt) cc_final: 0.7048 (tpp) REVERT: B 226 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7869 (mt-10) REVERT: B 254 ASP cc_start: 0.8519 (p0) cc_final: 0.7694 (t0) REVERT: N 5 GLN cc_start: 0.7644 (mp10) cc_final: 0.7401 (mp10) outliers start: 22 outliers final: 13 residues processed: 166 average time/residue: 0.0962 time to fit residues: 21.7262 Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN A 23 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131905 restraints weight = 8769.509| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.80 r_work: 0.3324 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8217 Z= 0.126 Angle : 0.477 5.694 11128 Z= 0.259 Chirality : 0.041 0.148 1271 Planarity : 0.004 0.048 1410 Dihedral : 4.398 33.902 1124 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.61 % Allowed : 12.16 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.27), residues: 1001 helix: 2.40 (0.25), residues: 420 sheet: 0.26 (0.34), residues: 232 loop : 0.36 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.014 0.001 TYR A 339 PHE 0.016 0.002 PHE N 108 TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8213) covalent geometry : angle 0.47651 / 0.26 (11120) SS BOND : bond 0.00216 / 0.13 ( 4) SS BOND : angle 0.80347 / 0.51 ( 8) hydrogen bonds : bond 0.03721 / 2.52 ( 441) hydrogen bonds : angle 4.09199 / 2.94 ( 1245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.4904 (mm) REVERT: R 161 MET cc_start: 0.7395 (mmt) cc_final: 0.7136 (tpp) REVERT: B 226 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7902 (mt-10) REVERT: N 5 GLN cc_start: 0.7641 (mp10) cc_final: 0.7406 (mp10) REVERT: N 105 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6890 (mtp180) outliers start: 23 outliers final: 16 residues processed: 162 average time/residue: 0.0997 time to fit residues: 21.7363 Evaluate side-chains 165 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129879 restraints weight = 8776.282| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.73 r_work: 0.3265 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8217 Z= 0.174 Angle : 0.523 6.740 11128 Z= 0.284 Chirality : 0.042 0.172 1271 Planarity : 0.004 0.047 1410 Dihedral : 4.645 34.624 1124 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.73 % Allowed : 12.39 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1001 helix: 2.27 (0.25), residues: 421 sheet: 0.09 (0.33), residues: 237 loop : 0.28 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.018 0.002 TYR A 311 PHE 0.024 0.002 PHE N 108 TRP 0.019 0.002 TRP B 339 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 8213) covalent geometry : angle 0.52289 / 0.28 (11120) SS BOND : bond 0.00238 / 0.14 ( 4) SS BOND : angle 1.03393 / 0.63 ( 8) hydrogen bonds : bond 0.04033 / 2.74 ( 441) hydrogen bonds : angle 4.26956 / 3.07 ( 1245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.4968 (mm) REVERT: R 161 MET cc_start: 0.7510 (mmt) cc_final: 0.7267 (tpp) REVERT: N 5 GLN cc_start: 0.7722 (mp10) cc_final: 0.7493 (mp10) outliers start: 24 outliers final: 19 residues processed: 163 average time/residue: 0.1016 time to fit residues: 22.3490 Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 200 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.172064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134628 restraints weight = 8718.404| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.73 r_work: 0.3355 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8217 Z= 0.104 Angle : 0.464 6.563 11128 Z= 0.250 Chirality : 0.040 0.150 1271 Planarity : 0.004 0.048 1410 Dihedral : 4.386 34.337 1124 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.82 % Allowed : 13.52 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.27), residues: 1001 helix: 2.43 (0.25), residues: 422 sheet: 0.12 (0.33), residues: 234 loop : 0.26 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.012 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.023 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 8213) covalent geometry : angle 0.46391 / 0.25 (11120) SS BOND : bond 0.00236 / 0.14 ( 4) SS BOND : angle 0.69829 / 0.45 ( 8) hydrogen bonds : bond 0.03566 / 2.40 ( 441) hydrogen bonds : angle 4.06400 / 2.91 ( 1245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.4950 (mm) REVERT: R 161 MET cc_start: 0.7296 (mmt) cc_final: 0.7047 (tpp) REVERT: B 59 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8503 (t80) REVERT: B 226 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 254 ASP cc_start: 0.8484 (p0) cc_final: 0.7675 (t0) REVERT: G 47 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8017 (mt-10) REVERT: N 5 GLN cc_start: 0.7678 (mp10) cc_final: 0.7458 (mp10) outliers start: 16 outliers final: 12 residues processed: 157 average time/residue: 0.0983 time to fit residues: 20.8410 Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133371 restraints weight = 8775.208| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.71 r_work: 0.3332 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8217 Z= 0.117 Angle : 0.476 8.178 11128 Z= 0.256 Chirality : 0.040 0.146 1271 Planarity : 0.004 0.047 1410 Dihedral : 4.367 33.823 1124 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.82 % Allowed : 13.64 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.27), residues: 1001 helix: 2.44 (0.25), residues: 422 sheet: 0.11 (0.33), residues: 234 loop : 0.27 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 356 TYR 0.012 0.001 TYR N 95 PHE 0.014 0.001 PHE N 108 TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 8213) covalent geometry : angle 0.47582 / 0.26 (11120) SS BOND : bond 0.00224 / 0.13 ( 4) SS BOND : angle 0.76017 / 0.49 ( 8) hydrogen bonds : bond 0.03643 / 2.46 ( 441) hydrogen bonds : angle 4.07613 / 2.92 ( 1245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.4932 (mm) REVERT: R 161 MET cc_start: 0.7411 (mmt) cc_final: 0.7180 (tpp) REVERT: B 59 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8483 (t80) REVERT: B 96 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7785 (ttp-170) REVERT: B 226 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 254 ASP cc_start: 0.8501 (p0) cc_final: 0.7730 (t0) REVERT: G 47 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8043 (mt-10) REVERT: N 5 GLN cc_start: 0.7704 (mp10) cc_final: 0.7489 (mp10) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.0997 time to fit residues: 21.0751 Evaluate side-chains 160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 200 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134992 restraints weight = 8686.731| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.74 r_work: 0.3364 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8217 Z= 0.104 Angle : 0.464 7.086 11128 Z= 0.250 Chirality : 0.040 0.138 1271 Planarity : 0.004 0.051 1410 Dihedral : 4.282 33.809 1124 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 13.98 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.27), residues: 1001 helix: 2.56 (0.25), residues: 420 sheet: 0.04 (0.34), residues: 234 loop : 0.28 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 356 TYR 0.011 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 8213) covalent geometry : angle 0.46393 / 0.25 (11120) SS BOND : bond 0.00263 / 0.15 ( 4) SS BOND : angle 0.84301 / 0.51 ( 8) hydrogen bonds : bond 0.03521 / 2.37 ( 441) hydrogen bonds : angle 3.99925 / 2.86 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.82 seconds wall clock time: 42 minutes 25.33 seconds (2545.33 seconds total)