Starting phenix.real_space_refine on Tue Mar 3 19:05:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f58_31461/03_2026/7f58_31461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f58_31461/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2026/7f58_31461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2026/7f58_31461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2026/7f58_31461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.76, per 1000 atoms: 0.22 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: 0.74 Conformation dependent library (CDL) restraints added in 300.1 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: 0.38 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: 1.27 Time building geometry restraints manager: 0.93 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 - 21.97: 4691 21.97 - 43.94: 199 43.94 - 65.92: 44 65.92 - 87.89: 9 87.89 - 109.86: 3 Dihedral angle restraints: 4946 sinusoidal: 1974 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=" N07 1I8 R 601 " pdb=" C28 1I8 R 601 " pdb=" C29 1I8 R 601 " pdb=" N09 1I8 R 601 " ideal model delta sinusoidal sigma weight residual -1.56 108.30 -109.86 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4943 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: 0.440 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 13.303 109.858 3008 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 covalent geometry : bond 0.00783 ( 8213) covalent geometry : angle 0.78963 (11120) SS BOND : bond 0.00223 ( 4) SS BOND : angle 2.00527 ( 8) hydrogen bonds : bond 0.14286 ( 441) hydrogen bonds : angle 6.16111 ( 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 : 0.298 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: 0.1053 time to fit residues: 28.3215 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 : 0.266 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3907 r_free = 0.3907 target = 0.169561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132451 restraints weight = 8699.580| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.70 r_work: 0.3302 rms_B_bonded: 2.80 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: 0.7920 moved from start: 0.1881 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= 0.187 Angle : 0.589 7.634 11128 Z= 0.321 Chirality : 0.044 0.164 1271 Planarity : 0.005 0.079 1410 Dihedral : 7.299 102.755 1161 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.82 % Allowed : 8.07 % Favored : 90.11 % 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: 1.89 (0.24), residues: 409 sheet: 0.56 (0.32), residues: 243 loop : 0.47 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.020 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 covalent geometry : bond 0.00416 ( 8213) covalent geometry : angle 0.58820 (11120) SS BOND : bond 0.00206 ( 4) SS BOND : angle 1.25685 ( 8) hydrogen bonds : bond 0.04763 ( 441) hydrogen bonds : angle 4.73380 ( 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 179 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: R 215 MET cc_start: 0.8609 (mtp) cc_final: 0.8400 (mtm) REVERT: R 220 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7442 (ttm-80) REVERT: A 343 ASP cc_start: 0.8353 (m-30) cc_final: 0.8043 (m-30) REVERT: B 97 SER cc_start: 0.8466 (p) cc_final: 0.8040 (m) REVERT: B 186 ASP cc_start: 0.7863 (m-30) cc_final: 0.7663 (m-30) REVERT: B 226 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 254 ASP cc_start: 0.8528 (p0) cc_final: 0.7758 (t0) REVERT: G 17 GLU cc_start: 0.8213 (pt0) cc_final: 0.7957 (pm20) REVERT: N 5 GLN cc_start: 0.7586 (mp10) cc_final: 0.7360 (mp10) outliers start: 16 outliers final: 10 residues processed: 172 average time/residue: 0.1063 time to fit residues: 24.1039 Evaluate side-chains 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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: 0.0970 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3929 r_free = 0.3929 target = 0.172288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134896 restraints weight = 8624.650| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.72 r_work: 0.3336 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8217 Z= 0.130 Angle : 0.503 7.541 11128 Z= 0.274 Chirality : 0.041 0.176 1271 Planarity : 0.004 0.062 1410 Dihedral : 6.839 100.463 1159 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.05 % Allowed : 9.43 % Favored : 88.52 % 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: 1.77 (0.26), residues: 1001 helix: 2.24 (0.24), residues: 410 sheet: 0.69 (0.34), residues: 224 loop : 0.36 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.015 0.001 TYR A 339 PHE 0.014 0.001 PHE N 108 TRP 0.017 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8213) covalent geometry : angle 0.50284 (11120) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.91201 ( 8) hydrogen bonds : bond 0.04101 ( 441) hydrogen bonds : angle 4.42338 ( 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 175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7385 (ttm-80) REVERT: A 343 ASP cc_start: 0.8284 (m-30) cc_final: 0.7988 (m-30) REVERT: A 356 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7955 (mtm110) REVERT: B 59 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8400 (t80) REVERT: B 226 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7786 (mt-10) REVERT: G 17 GLU cc_start: 0.8203 (pt0) cc_final: 0.7927 (pm20) REVERT: N 5 GLN cc_start: 0.7577 (mp10) cc_final: 0.7099 (mp10) outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 0.1001 time to fit residues: 22.4889 Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 92 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 B residue 331 SER 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: 3.9990 chunk 67 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3910 r_free = 0.3910 target = 0.170502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133889 restraints weight = 8759.533| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.69 r_work: 0.3333 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8217 Z= 0.126 Angle : 0.484 6.855 11128 Z= 0.263 Chirality : 0.041 0.161 1271 Planarity : 0.004 0.056 1410 Dihedral : 6.669 96.459 1159 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.95 % Allowed : 10.00 % Favored : 87.05 % 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 (0.26), residues: 1001 helix: 2.31 (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 0.003 0.000 ARG B 46 TYR 0.015 0.001 TYR A 339 PHE 0.014 0.001 PHE N 108 TRP 0.015 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8213) covalent geometry : angle 0.48333 (11120) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.83240 ( 8) hydrogen bonds : bond 0.03887 ( 441) hydrogen bonds : angle 4.29040 ( 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 179 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5291 (mm) REVERT: R 200 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6873 (ptp) REVERT: A 356 ARG cc_start: 0.8253 (mtm110) cc_final: 0.8004 (mtm110) REVERT: B 49 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8332 (mtt90) REVERT: N 5 GLN cc_start: 0.7616 (mp10) cc_final: 0.7381 (mp10) outliers start: 26 outliers final: 20 residues processed: 168 average time/residue: 0.1055 time to fit residues: 23.5485 Evaluate side-chains 165 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 79 MET 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 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 49 ARG 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 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 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: 0.7980 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3925 r_free = 0.3925 target = 0.171977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135116 restraints weight = 8662.950| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.71 r_work: 0.3347 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8217 Z= 0.111 Angle : 0.459 6.356 11128 Z= 0.250 Chirality : 0.040 0.150 1271 Planarity : 0.004 0.052 1410 Dihedral : 6.468 93.440 1159 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.50 % Allowed : 11.70 % Favored : 85.80 % 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: 1.78 (0.27), residues: 1001 helix: 2.44 (0.24), residues: 414 sheet: 0.43 (0.34), residues: 226 loop : 0.29 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.013 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8213) covalent geometry : angle 0.45871 (11120) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.70678 ( 8) hydrogen bonds : bond 0.03696 ( 441) hydrogen bonds : angle 4.15277 ( 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 172 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5109 (mm) REVERT: A 21 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 226 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 254 ASP cc_start: 0.8522 (p0) cc_final: 0.7687 (t0) REVERT: N 5 GLN cc_start: 0.7596 (mp10) cc_final: 0.7353 (mp10) outliers start: 22 outliers final: 15 residues processed: 160 average time/residue: 0.1064 time to fit residues: 22.5447 Evaluate side-chains 161 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 79 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 G residue 52 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133087 restraints weight = 8668.402| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.72 r_work: 0.3325 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2820 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= 0.130 Angle : 0.475 6.337 11128 Z= 0.258 Chirality : 0.041 0.157 1271 Planarity : 0.004 0.049 1410 Dihedral : 6.473 91.449 1159 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.30 % Allowed : 11.82 % 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: 1.71 (0.27), residues: 1001 helix: 2.35 (0.25), residues: 420 sheet: 0.38 (0.34), residues: 225 loop : 0.26 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.015 0.001 TYR A 339 PHE 0.017 0.002 PHE N 108 TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8213) covalent geometry : angle 0.47460 (11120) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.79940 ( 8) hydrogen bonds : bond 0.03793 ( 441) hydrogen bonds : angle 4.17886 ( 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 185 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.4993 (mm) REVERT: A 21 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7203 (mm-30) REVERT: B 226 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 254 ASP cc_start: 0.8531 (p0) cc_final: 0.7698 (t0) REVERT: N 5 GLN cc_start: 0.7654 (mp10) cc_final: 0.7412 (mp10) REVERT: N 105 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6853 (mtp180) outliers start: 29 outliers final: 22 residues processed: 173 average time/residue: 0.1020 time to fit residues: 23.6522 Evaluate side-chains 169 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 228 VAL 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 255 LEU Chi-restraints excluded: chain B residue 275 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 Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 74 ASN A 23 ASN A 31 GLN A 59 GLN A 267 GLN A 371 ASN B 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129542 restraints weight = 8822.413| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.68 r_work: 0.3259 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8217 Z= 0.188 Angle : 0.531 6.286 11128 Z= 0.289 Chirality : 0.043 0.175 1271 Planarity : 0.004 0.047 1410 Dihedral : 6.658 92.696 1159 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.64 % Allowed : 12.27 % Favored : 84.09 % 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: 1.47 (0.27), residues: 1001 helix: 2.17 (0.24), residues: 421 sheet: 0.17 (0.33), residues: 232 loop : 0.17 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.018 0.002 TYR A 311 PHE 0.026 0.002 PHE N 108 TRP 0.017 0.002 TRP B 339 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8213) covalent geometry : angle 0.53060 (11120) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.03358 ( 8) hydrogen bonds : bond 0.04122 ( 441) hydrogen bonds : angle 4.33817 ( 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 177 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.4840 (mm) REVERT: A 20 ARG cc_start: 0.7391 (mtm110) cc_final: 0.7162 (mtm110) REVERT: A 21 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 226 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8075 (mt-10) REVERT: N 5 GLN cc_start: 0.7687 (mp10) cc_final: 0.7452 (mp10) outliers start: 32 outliers final: 24 residues processed: 164 average time/residue: 0.1053 time to fit residues: 23.0407 Evaluate side-chains 167 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 200 MET Chi-restraints excluded: chain R residue 228 VAL 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 40 THR 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 42 ARG 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 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 chunk 23 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 294 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136382 restraints weight = 8713.356| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.70 r_work: 0.3377 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8217 Z= 0.093 Angle : 0.448 6.902 11128 Z= 0.243 Chirality : 0.040 0.134 1271 Planarity : 0.004 0.048 1410 Dihedral : 6.270 86.669 1159 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.39 % Allowed : 13.75 % Favored : 83.86 % 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: 1.72 (0.27), residues: 1001 helix: 2.50 (0.25), residues: 420 sheet: 0.22 (0.35), residues: 214 loop : 0.20 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.011 0.001 TYR R 80 PHE 0.011 0.001 PHE B 199 TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 8213) covalent geometry : angle 0.44798 (11120) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.57738 ( 8) hydrogen bonds : bond 0.03435 ( 441) hydrogen bonds : angle 4.02423 ( 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 173 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.4940 (mm) REVERT: R 280 PHE cc_start: 0.8092 (t80) cc_final: 0.7748 (t80) REVERT: B 59 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8466 (t80) REVERT: B 96 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7745 (ttm-80) REVERT: B 226 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 254 ASP cc_start: 0.8488 (p0) cc_final: 0.7698 (t0) REVERT: G 47 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8015 (mt-10) REVERT: N 5 GLN cc_start: 0.7644 (mp10) cc_final: 0.7421 (mp10) outliers start: 21 outliers final: 14 residues processed: 165 average time/residue: 0.0947 time to fit residues: 21.0057 Evaluate side-chains 160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 79 MET 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 42 ARG 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 275 SER 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: 0.0970 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130365 restraints weight = 8774.558| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.71 r_work: 0.3281 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8217 Z= 0.166 Angle : 0.519 7.892 11128 Z= 0.281 Chirality : 0.042 0.168 1271 Planarity : 0.004 0.047 1410 Dihedral : 6.473 88.203 1159 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.50 % Allowed : 13.41 % Favored : 84.09 % 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: 2.34 (0.24), residues: 421 sheet: 0.03 (0.33), residues: 237 loop : 0.22 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 356 TYR 0.016 0.001 TYR A 339 PHE 0.022 0.002 PHE N 108 TRP 0.021 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8213) covalent geometry : angle 0.51874 (11120) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.93025 ( 8) hydrogen bonds : bond 0.03955 ( 441) hydrogen bonds : angle 4.20581 ( 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 169 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.4979 (mm) REVERT: R 280 PHE cc_start: 0.8190 (t80) cc_final: 0.7783 (t80) REVERT: A 20 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7165 (mtm110) REVERT: A 356 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7893 (mtm110) REVERT: B 59 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8551 (t80) REVERT: B 226 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8110 (mt-10) REVERT: G 47 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8074 (mt-10) REVERT: N 5 GLN cc_start: 0.7705 (mp10) cc_final: 0.7488 (mp10) REVERT: N 43 LYS cc_start: 0.6432 (mmmt) cc_final: 0.6157 (mmmt) outliers start: 22 outliers final: 18 residues processed: 159 average time/residue: 0.1006 time to fit residues: 21.4519 Evaluate side-chains 165 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 79 MET 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 42 ARG 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 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 78 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: 0.9980 chunk 57 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.169230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133135 restraints weight = 8797.411| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.68 r_work: 0.3314 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8217 Z= 0.124 Angle : 0.481 6.273 11128 Z= 0.261 Chirality : 0.041 0.155 1271 Planarity : 0.004 0.047 1410 Dihedral : 6.361 86.136 1159 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.27 % Allowed : 13.86 % Favored : 83.86 % 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: 1.61 (0.27), residues: 1001 helix: 2.41 (0.25), residues: 420 sheet: 0.06 (0.33), residues: 235 loop : 0.21 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.013 0.001 TYR A 339 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 covalent geometry : bond 0.00275 ( 8213) covalent geometry : angle 0.48082 (11120) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.77649 ( 8) hydrogen bonds : bond 0.03711 ( 441) hydrogen bonds : angle 4.10326 ( 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 165 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.4994 (mm) REVERT: R 280 PHE cc_start: 0.8142 (t80) cc_final: 0.7753 (t80) REVERT: A 356 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7891 (mtm110) REVERT: B 59 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8553 (t80) REVERT: B 226 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8052 (mt-10) REVERT: B 254 ASP cc_start: 0.8495 (p0) cc_final: 0.7710 (t0) REVERT: G 47 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8064 (mt-10) REVERT: N 5 GLN cc_start: 0.7713 (mp10) cc_final: 0.7507 (mp10) outliers start: 20 outliers final: 17 residues processed: 156 average time/residue: 0.0984 time to fit residues: 20.5240 Evaluate side-chains 164 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 79 MET 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 205 SER 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 42 ARG 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 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 78 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: 0.6980 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN 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 = 0.171893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135649 restraints weight = 8720.966| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.70 r_work: 0.3376 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8217 Z= 0.100 Angle : 0.454 5.987 11128 Z= 0.247 Chirality : 0.040 0.134 1271 Planarity : 0.004 0.048 1410 Dihedral : 6.150 80.648 1159 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.16 % Allowed : 13.86 % Favored : 83.98 % 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: 1.74 (0.27), residues: 1001 helix: 2.55 (0.25), residues: 420 sheet: 0.03 (0.33), residues: 238 loop : 0.33 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.010 0.001 TYR N 95 PHE 0.011 0.001 PHE R 262 TRP 0.022 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8213) covalent geometry : angle 0.45415 (11120) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.64495 ( 8) hydrogen bonds : bond 0.03472 ( 441) hydrogen bonds : angle 3.97591 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.26 seconds wall clock time: 42 minutes 5.14 seconds (2525.14 seconds total)