Starting phenix.real_space_refine on Wed Mar 12 19:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f58_31461/03_2025/7f58_31461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f58_31461/03_2025/7f58_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2025/7f58_31461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2025/7f58_31461.map" model { file = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2025/7f58_31461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f58_31461/03_2025/7f58_31461.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.79, per 1000 atoms: 0.97 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: 2.71 Conformation dependent library (CDL) restraints added in 952.0 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: 0.88 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: 4.43 Time building geometry restraints manager: 3.25 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: 84.630 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.900 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.460 ------------------------------------------------------------------------------- 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 8213 Z= 0.524 Angle : 0.790 9.956 11120 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 : 9.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (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 TRP 0.024 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 262 TYR 0.020 0.002 TYR A 339 ARG 0.008 0.001 ARG N 72 *********************** 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 : 0.871 Fit side-chains revert: symmetry clash REVERT: R 215 MET cc_start: 0.8368 (mtp) cc_final: 0.8129 (mtm) REVERT: R 220 ARG cc_start: 0.7076 (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: 0.3507 time to fit residues: 95.0182 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 : 1.541 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135866 restraints weight = 8610.838| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.73 r_work: 0.3347 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8213 Z= 0.198 Angle : 0.551 7.398 11120 Z= 0.301 Chirality : 0.043 0.156 1271 Planarity : 0.005 0.082 1410 Dihedral : 7.140 103.382 1161 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.48 % Allowed : 8.18 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.26), residues: 1001 helix: 2.01 (0.24), residues: 410 sheet: 0.76 (0.34), residues: 221 loop : 0.44 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE N 68 TYR 0.017 0.001 TYR A 339 ARG 0.007 0.001 ARG B 49 *********************** 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: 13 poor density : 166 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7430 (ttm-80) REVERT: A 221 MET cc_start: 0.8813 (ttm) cc_final: 0.8591 (ttp) REVERT: A 343 ASP cc_start: 0.8355 (m-30) cc_final: 0.8058 (m-30) REVERT: B 97 SER cc_start: 0.8459 (p) cc_final: 0.8003 (m) REVERT: B 186 ASP cc_start: 0.7791 (m-30) cc_final: 0.7564 (m-30) REVERT: B 254 ASP cc_start: 0.8556 (p0) cc_final: 0.7763 (t0) REVERT: B 268 ASN cc_start: 0.8072 (m110) cc_final: 0.7861 (m-40) REVERT: G 17 GLU cc_start: 0.8265 (pt0) cc_final: 0.7990 (pm20) REVERT: G 47 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7894 (mt-10) REVERT: N 5 GLN cc_start: 0.7579 (mp10) cc_final: 0.7369 (mp10) REVERT: N 33 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8581 (ttpt) outliers start: 13 outliers final: 7 residues processed: 173 average time/residue: 0.2212 time to fit residues: 51.0363 Evaluate side-chains 157 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 367 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132647 restraints weight = 8741.114| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.71 r_work: 0.3310 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8213 Z= 0.235 Angle : 0.532 7.286 11120 Z= 0.289 Chirality : 0.042 0.185 1271 Planarity : 0.004 0.063 1410 Dihedral : 6.899 100.707 1159 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.82 % Allowed : 9.20 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1001 helix: 2.16 (0.24), residues: 409 sheet: 0.57 (0.32), residues: 241 loop : 0.41 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.009 0.001 HIS A 357 PHE 0.022 0.002 PHE N 108 TYR 0.018 0.001 TYR A 339 ARG 0.002 0.000 ARG B 46 *********************** 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 174 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7427 (ttm-80) REVERT: A 343 ASP cc_start: 0.8253 (m-30) cc_final: 0.7957 (m-30) REVERT: A 356 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7961 (mtm110) REVERT: B 186 ASP cc_start: 0.7829 (m-30) cc_final: 0.7548 (m-30) REVERT: B 226 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 254 ASP cc_start: 0.8507 (p0) cc_final: 0.7707 (t0) REVERT: G 17 GLU cc_start: 0.8210 (pt0) cc_final: 0.7956 (pm20) REVERT: N 5 GLN cc_start: 0.7567 (mp10) cc_final: 0.7312 (mp10) outliers start: 16 outliers final: 14 residues processed: 168 average time/residue: 0.2459 time to fit residues: 55.3148 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 : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 309 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 32 GLN B 44 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133426 restraints weight = 8678.343| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.68 r_work: 0.3323 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8213 Z= 0.191 Angle : 0.493 7.000 11120 Z= 0.268 Chirality : 0.041 0.168 1271 Planarity : 0.004 0.057 1410 Dihedral : 6.733 97.577 1159 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.39 % Allowed : 10.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1001 helix: 2.23 (0.24), residues: 413 sheet: 0.46 (0.33), residues: 231 loop : 0.35 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE N 108 TYR 0.015 0.001 TYR A 339 ARG 0.003 0.000 ARG B 46 *********************** 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 175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7365 (ttm-80) REVERT: A 356 ARG cc_start: 0.8213 (mtm110) cc_final: 0.7979 (mtm110) REVERT: B 46 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8344 (ttm110) REVERT: B 49 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8318 (mtt90) REVERT: G 17 GLU cc_start: 0.8226 (pt0) cc_final: 0.7982 (pm20) REVERT: N 5 GLN cc_start: 0.7588 (mp10) cc_final: 0.7334 (mp10) outliers start: 21 outliers final: 18 residues processed: 166 average time/residue: 0.2371 time to fit residues: 52.6725 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 : 0.947 ------------------------------------------------------------------------------- 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 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 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 37 VAL 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 43 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130265 restraints weight = 8507.961| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.70 r_work: 0.3287 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8213 Z= 0.253 Angle : 0.524 6.734 11120 Z= 0.284 Chirality : 0.042 0.182 1271 Planarity : 0.004 0.053 1410 Dihedral : 6.768 96.753 1159 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.64 % Allowed : 11.59 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1001 helix: 2.11 (0.24), residues: 419 sheet: 0.39 (0.33), residues: 223 loop : 0.19 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.023 0.002 PHE N 108 TYR 0.018 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 *********************** 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 181 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5172 (mm) REVERT: R 220 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7439 (ttm-80) REVERT: A 356 ARG cc_start: 0.8236 (mtm110) cc_final: 0.8010 (mtm110) REVERT: B 49 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8250 (mtt90) REVERT: B 186 ASP cc_start: 0.7900 (m-30) cc_final: 0.7595 (m-30) REVERT: B 226 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 254 ASP cc_start: 0.8499 (p0) cc_final: 0.7677 (t0) REVERT: B 270 ILE cc_start: 0.8935 (pt) cc_final: 0.8724 (pt) REVERT: G 17 GLU cc_start: 0.8204 (pt0) cc_final: 0.7932 (pm20) REVERT: N 5 GLN cc_start: 0.7647 (mp10) cc_final: 0.7404 (mp10) outliers start: 32 outliers final: 25 residues processed: 166 average time/residue: 0.2169 time to fit residues: 47.9437 Evaluate side-chains 170 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 309 LEU 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 367 VAL 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 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 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130933 restraints weight = 8709.464| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.68 r_work: 0.3280 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8213 Z= 0.210 Angle : 0.500 7.236 11120 Z= 0.271 Chirality : 0.041 0.175 1271 Planarity : 0.004 0.051 1410 Dihedral : 6.674 95.173 1159 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.52 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 1001 helix: 2.20 (0.24), residues: 421 sheet: 0.26 (0.33), residues: 229 loop : 0.19 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE N 108 TYR 0.015 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 *********************** 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 183 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5052 (mm) REVERT: A 356 ARG cc_start: 0.8241 (mtm110) cc_final: 0.8030 (mtm110) REVERT: B 197 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7158 (ttp80) REVERT: N 5 GLN cc_start: 0.7657 (mp10) cc_final: 0.7419 (mp10) outliers start: 31 outliers final: 21 residues processed: 169 average time/residue: 0.2179 time to fit residues: 49.0463 Evaluate side-chains 165 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 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 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 331 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130840 restraints weight = 8730.350| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.69 r_work: 0.3286 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8213 Z= 0.205 Angle : 0.501 7.071 11120 Z= 0.272 Chirality : 0.041 0.171 1271 Planarity : 0.004 0.049 1410 Dihedral : 6.622 93.682 1159 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.30 % Allowed : 12.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 1001 helix: 2.22 (0.24), residues: 419 sheet: 0.13 (0.33), residues: 231 loop : 0.18 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE N 108 TYR 0.014 0.001 TYR A 339 ARG 0.003 0.000 ARG B 49 *********************** 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 179 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5044 (mm) REVERT: A 21 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 356 ARG cc_start: 0.8241 (mtm110) cc_final: 0.8031 (mtm110) REVERT: B 197 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7216 (ttp80) REVERT: N 5 GLN cc_start: 0.7691 (mp10) cc_final: 0.7464 (mp10) outliers start: 29 outliers final: 21 residues processed: 167 average time/residue: 0.2121 time to fit residues: 47.7855 Evaluate side-chains 167 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 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 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 N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132145 restraints weight = 8821.037| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.71 r_work: 0.3306 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8213 Z= 0.168 Angle : 0.481 7.003 11120 Z= 0.261 Chirality : 0.041 0.158 1271 Planarity : 0.004 0.048 1410 Dihedral : 6.472 90.669 1159 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.95 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1001 helix: 2.35 (0.25), residues: 420 sheet: 0.15 (0.33), residues: 231 loop : 0.18 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.005 0.000 ARG B 49 *********************** 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 176 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.4825 (mm) REVERT: R 280 PHE cc_start: 0.8170 (t80) cc_final: 0.7689 (t80) REVERT: R 281 MET cc_start: 0.8612 (mmt) cc_final: 0.7379 (mmt) REVERT: B 197 ARG cc_start: 0.7433 (ttp80) cc_final: 0.7189 (ttp80) REVERT: G 47 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8065 (mt-10) REVERT: N 5 GLN cc_start: 0.7680 (mp10) cc_final: 0.7472 (mp10) outliers start: 26 outliers final: 22 residues processed: 163 average time/residue: 0.2230 time to fit residues: 49.4976 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 : 0.882 ------------------------------------------------------------------------------- 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 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 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 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 30 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132160 restraints weight = 8820.139| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.71 r_work: 0.3320 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8213 Z= 0.160 Angle : 0.477 6.703 11120 Z= 0.259 Chirality : 0.040 0.151 1271 Planarity : 0.004 0.049 1410 Dihedral : 6.358 87.299 1159 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.61 % Allowed : 12.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1001 helix: 2.36 (0.25), residues: 422 sheet: 0.10 (0.33), residues: 230 loop : 0.18 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.008 0.000 ARG A 356 *********************** 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 173 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5780 (tt) cc_final: 0.4927 (mm) REVERT: R 280 PHE cc_start: 0.8119 (t80) cc_final: 0.7741 (t80) REVERT: R 281 MET cc_start: 0.8671 (mmt) cc_final: 0.7447 (mmt) REVERT: B 197 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7150 (ttp80) REVERT: B 226 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 254 ASP cc_start: 0.8501 (p0) cc_final: 0.7698 (t0) REVERT: G 47 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8033 (mt-10) REVERT: N 5 GLN cc_start: 0.7708 (mp10) cc_final: 0.7498 (mp10) outliers start: 23 outliers final: 20 residues processed: 162 average time/residue: 0.2128 time to fit residues: 46.2094 Evaluate side-chains 164 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 G residue 30 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.0970 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131103 restraints weight = 8744.273| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.69 r_work: 0.3287 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8213 Z= 0.217 Angle : 0.515 6.700 11120 Z= 0.278 Chirality : 0.041 0.163 1271 Planarity : 0.004 0.048 1410 Dihedral : 6.457 87.579 1159 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.73 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1001 helix: 2.34 (0.25), residues: 419 sheet: -0.02 (0.33), residues: 237 loop : 0.17 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE N 108 TYR 0.015 0.001 TYR A 339 ARG 0.010 0.000 ARG A 356 ********************** 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 167 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: R 44 LEU cc_start: 0.5837 (tt) cc_final: 0.4945 (mm) REVERT: R 280 PHE cc_start: 0.8100 (t80) cc_final: 0.7759 (t80) REVERT: R 281 MET cc_start: 0.8719 (mmt) cc_final: 0.7646 (mmt) REVERT: B 197 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7227 (ttp80) REVERT: G 47 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8069 (mt-10) REVERT: N 5 GLN cc_start: 0.7730 (mp10) cc_final: 0.7521 (mp10) outliers start: 24 outliers final: 22 residues processed: 157 average time/residue: 0.2188 time to fit residues: 46.2470 Evaluate side-chains 166 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 ASN 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 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 N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 59 GLN A 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.168330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132002 restraints weight = 8817.042| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.69 r_work: 0.3304 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8213 Z= 0.182 Angle : 0.499 6.777 11120 Z= 0.269 Chirality : 0.041 0.159 1271 Planarity : 0.004 0.048 1410 Dihedral : 6.402 86.351 1159 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.61 % Allowed : 13.07 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 1001 helix: 2.39 (0.25), residues: 420 sheet: -0.03 (0.33), residues: 237 loop : 0.18 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE N 108 TYR 0.013 0.001 TYR A 339 ARG 0.014 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4998.39 seconds wall clock time: 88 minutes 56.78 seconds (5336.78 seconds total)