Starting phenix.real_space_refine on Tue Mar 3 17:24:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xml_33300/03_2026/7xml_33300.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xml_33300/03_2026/7xml_33300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xml_33300/03_2026/7xml_33300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xml_33300/03_2026/7xml_33300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xml_33300/03_2026/7xml_33300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xml_33300/03_2026/7xml_33300.map" } resolution = 3.2 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= 0.009 sd= 0.227 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 24 5.16 5 C 4794 2.51 5 N 1264 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 7626 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3258 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "B" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3258 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.26 Number of scatterers: 7626 At special positions: 0 Unit cell: (134.48, 104.14, 77.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 Mg 2 11.99 O 1542 8.00 N 1264 7.00 C 4794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.72 Conformation dependent library (CDL) restraints added in 340.1 milliseconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 40.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 removed outlier: 4.041A pdb=" N ASN A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.532A pdb=" N ILE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.686A pdb=" N ILE A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 122 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.750A pdb=" N ALA A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.713A pdb=" N GLY A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.566A pdb=" N VAL A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.856A pdb=" N ASP A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.987A pdb=" N LEU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.662A pdb=" N VAL A 318 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 4.191A pdb=" N LYS A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.686A pdb=" N PHE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.784A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.904A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.000A pdb=" N SER A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.042A pdb=" N ASN B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.532A pdb=" N ILE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.686A pdb=" N ILE B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 122 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 153 through 156 removed outlier: 3.749A pdb=" N ALA B 156 " --> pdb=" O GLY B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 174 through 197 removed outlier: 3.713A pdb=" N GLY B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.566A pdb=" N VAL B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.855A pdb=" N ASP B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.987A pdb=" N LEU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.663A pdb=" N VAL B 318 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 4.190A pdb=" N LYS B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.686A pdb=" N PHE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 359 " --> pdb=" O MET B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.784A pdb=" N VAL B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.904A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.999A pdb=" N SER B 424 " --> pdb=" O GLY B 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 13 removed outlier: 4.127A pdb=" N ASP A 6 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 21 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.926A pdb=" N LEU A 142 " --> pdb=" O GLN A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 151 removed outlier: 6.871A pdb=" N PHE A 165 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 168 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 283 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 239 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 285 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 335 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 313 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 337 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 336 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER A 366 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 338 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN A 388 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 250 removed outlier: 3.693A pdb=" N LYS A 255 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 16 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 13 removed outlier: 4.127A pdb=" N ASP B 6 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 21 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.926A pdb=" N LEU B 142 " --> pdb=" O GLN B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 151 removed outlier: 6.871A pdb=" N PHE B 165 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 168 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE B 283 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 239 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 285 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 335 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 313 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B 337 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 336 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER B 366 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 338 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 388 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 removed outlier: 3.693A pdb=" N LYS B 255 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 20 280 hydrogen bonds defined for protein. 798 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: 1.25 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: 1.22 - 1.34: 2481 1.34 - 1.45: 967 1.45 - 1.57: 4252 1.57 - 1.69: 0 1.69 - 1.80: 46 Bond restraints: 7746 Sorted by residual: bond pdb=" CA SER B 139 " pdb=" CB SER B 139 " ideal model delta sigma weight residual 1.527 1.466 0.061 1.75e-02 3.27e+03 1.20e+01 bond pdb=" CA SER A 139 " pdb=" CB SER A 139 " ideal model delta sigma weight residual 1.527 1.466 0.061 1.75e-02 3.27e+03 1.20e+01 bond pdb=" CB VAL A 312 " pdb=" CG2 VAL A 312 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB VAL B 312 " pdb=" CG2 VAL B 312 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB ASP A 374 " pdb=" CG ASP A 374 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.07e+00 ... (remaining 7741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 10293 2.78 - 5.57: 181 5.57 - 8.35: 24 8.35 - 11.13: 0 11.13 - 13.92: 2 Bond angle restraints: 10500 Sorted by residual: angle pdb=" CA LEU A 60 " pdb=" CB LEU A 60 " pdb=" CG LEU A 60 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" CA LEU B 60 " pdb=" CB LEU B 60 " pdb=" CG LEU B 60 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" N ILE A 284 " pdb=" CA ILE A 284 " pdb=" C ILE A 284 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" N ILE B 284 " pdb=" CA ILE B 284 " pdb=" C ILE B 284 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" C THR B 372 " pdb=" N GLU B 373 " pdb=" CA GLU B 373 " ideal model delta sigma weight residual 121.54 128.64 -7.10 1.91e+00 2.74e-01 1.38e+01 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 4375 14.53 - 29.06: 197 29.06 - 43.59: 66 43.59 - 58.12: 8 58.12 - 72.65: 4 Dihedral angle restraints: 4650 sinusoidal: 1826 harmonic: 2824 Sorted by residual: dihedral pdb=" CA GLU A 373 " pdb=" C GLU A 373 " pdb=" N ASP A 374 " pdb=" CA ASP A 374 " ideal model delta harmonic sigma weight residual 180.00 132.21 47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA GLU B 373 " pdb=" C GLU B 373 " pdb=" N ASP B 374 " pdb=" CA ASP B 374 " ideal model delta harmonic sigma weight residual 180.00 132.21 47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ASN D 24 " pdb=" C ASN D 24 " pdb=" N PRO D 25 " pdb=" CA PRO D 25 " ideal model delta harmonic sigma weight residual 180.00 -144.48 -35.52 0 5.00e+00 4.00e-02 5.05e+01 ... (remaining 4647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 816 0.056 - 0.111: 302 0.111 - 0.167: 59 0.167 - 0.222: 7 0.222 - 0.278: 4 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CB VAL D 13 " pdb=" CA VAL D 13 " pdb=" CG1 VAL D 13 " pdb=" CG2 VAL D 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL C 13 " pdb=" CA VAL C 13 " pdb=" CG1 VAL C 13 " pdb=" CG2 VAL C 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE B 149 " pdb=" CA ILE B 149 " pdb=" CG1 ILE B 149 " pdb=" CG2 ILE B 149 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1185 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 350 " 0.008 2.00e-02 2.50e+03 1.60e-02 4.50e+00 pdb=" CG PHE B 350 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 350 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 350 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 350 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 350 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 350 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 350 " 0.008 2.00e-02 2.50e+03 1.60e-02 4.50e+00 pdb=" CG PHE A 350 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 350 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 350 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 350 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 350 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 350 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 374 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" CG ASP A 374 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP A 374 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 374 " 0.012 2.00e-02 2.50e+03 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2610 2.86 - 3.37: 6815 3.37 - 3.88: 11979 3.88 - 4.39: 13484 4.39 - 4.90: 24071 Nonbonded interactions: 58959 Sorted by model distance: nonbonded pdb=" OG SER A 267 " pdb=" OD2 ASP A 294 " model vdw 2.350 3.040 nonbonded pdb=" OG SER B 267 " pdb=" OD2 ASP B 294 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 139 " pdb=" OG SER A 139 " model vdw 2.368 3.040 nonbonded pdb=" O SER B 139 " pdb=" OG SER B 139 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASN B 138 " pdb=" NZ LYS B 140 " model vdw 2.369 3.120 ... (remaining 58954 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 428) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.980 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.009 0.073 7746 Z= 0.370 Angle : 0.932 13.919 10500 Z= 0.510 Chirality : 0.059 0.278 1188 Planarity : 0.006 0.046 1394 Dihedral : 10.107 72.648 2850 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.15 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.21 % 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: -4.61 (0.21), residues: 982 helix: -3.27 (0.17), residues: 360 sheet: -3.06 (0.34), residues: 130 loop : -2.84 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 52 TYR 0.014 0.002 TYR C 66 PHE 0.031 0.004 PHE B 350 TRP 0.021 0.003 TRP B 273 HIS 0.006 0.002 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00907 ( 7746) covalent geometry : angle 0.93231 (10500) hydrogen bonds : bond 0.21913 ( 280) hydrogen bonds : angle 7.66023 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 100 THR cc_start: 0.8098 (t) cc_final: 0.7732 (p) REVERT: A 164 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 292 GLU cc_start: 0.7097 (pm20) cc_final: 0.6877 (mm-30) REVERT: A 354 GLU cc_start: 0.7240 (tp30) cc_final: 0.6906 (tp30) REVERT: B 78 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 100 THR cc_start: 0.8107 (t) cc_final: 0.7739 (p) REVERT: B 164 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 292 GLU cc_start: 0.7085 (pm20) cc_final: 0.6875 (mm-30) REVERT: B 354 GLU cc_start: 0.7217 (tp30) cc_final: 0.6885 (tp30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1123 time to fit residues: 20.8738 Evaluate side-chains 89 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 257 HIS C 27 ASN B 187 HIS B 211 ASN B 257 HIS D 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139039 restraints weight = 8357.097| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.37 r_work: 0.3394 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7746 Z= 0.121 Angle : 0.558 7.759 10500 Z= 0.291 Chirality : 0.043 0.151 1188 Planarity : 0.004 0.036 1394 Dihedral : 5.579 35.926 1062 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.62 % Allowed : 7.88 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.24), residues: 982 helix: -1.86 (0.23), residues: 386 sheet: -2.40 (0.40), residues: 130 loop : -2.40 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 358 TYR 0.013 0.001 TYR D 66 PHE 0.010 0.002 PHE B 248 TRP 0.007 0.001 TRP A 273 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7746) covalent geometry : angle 0.55810 (10500) hydrogen bonds : bond 0.03652 ( 280) hydrogen bonds : angle 4.32119 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 0.0793 time to fit residues: 10.7315 Evaluate side-chains 83 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.181119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132916 restraints weight = 8470.016| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.42 r_work: 0.3243 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7746 Z= 0.257 Angle : 0.636 8.847 10500 Z= 0.332 Chirality : 0.047 0.154 1188 Planarity : 0.004 0.034 1394 Dihedral : 5.734 40.987 1062 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.48 % Allowed : 10.59 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.26), residues: 982 helix: -1.35 (0.26), residues: 386 sheet: -2.07 (0.44), residues: 130 loop : -2.35 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.016 0.002 TYR C 66 PHE 0.014 0.003 PHE A 248 TRP 0.010 0.002 TRP A 273 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 7746) covalent geometry : angle 0.63591 (10500) hydrogen bonds : bond 0.04470 ( 280) hydrogen bonds : angle 4.25116 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7944 (tt0) cc_final: 0.7592 (tt0) REVERT: B 22 GLU cc_start: 0.7945 (tt0) cc_final: 0.7608 (tt0) REVERT: D 46 GLU cc_start: 0.7438 (pp20) cc_final: 0.6759 (pm20) outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.0783 time to fit residues: 9.8432 Evaluate side-chains 80 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.182086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132874 restraints weight = 8538.715| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.54 r_work: 0.3245 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7746 Z= 0.191 Angle : 0.568 7.548 10500 Z= 0.294 Chirality : 0.045 0.142 1188 Planarity : 0.004 0.034 1394 Dihedral : 5.444 40.051 1062 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.97 % Allowed : 11.82 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.26), residues: 982 helix: -1.03 (0.27), residues: 386 sheet: -1.96 (0.46), residues: 130 loop : -2.28 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.015 0.001 TYR C 66 PHE 0.012 0.002 PHE B 248 TRP 0.008 0.001 TRP B 273 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 7746) covalent geometry : angle 0.56833 (10500) hydrogen bonds : bond 0.03554 ( 280) hydrogen bonds : angle 3.94089 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 0.0710 time to fit residues: 9.3253 Evaluate side-chains 73 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138386 restraints weight = 8462.162| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.37 r_work: 0.3328 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7746 Z= 0.111 Angle : 0.505 8.591 10500 Z= 0.263 Chirality : 0.042 0.173 1188 Planarity : 0.003 0.030 1394 Dihedral : 4.978 35.209 1062 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.35 % Allowed : 13.18 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.27), residues: 982 helix: -0.63 (0.28), residues: 386 sheet: -1.94 (0.46), residues: 134 loop : -2.07 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.010 0.001 TYR C 66 PHE 0.009 0.001 PHE A 248 TRP 0.005 0.001 TRP A 273 HIS 0.002 0.000 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7746) covalent geometry : angle 0.50546 (10500) hydrogen bonds : bond 0.02715 ( 280) hydrogen bonds : angle 3.59925 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.6638 (pm20) cc_final: 0.6359 (pm20) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 0.0811 time to fit residues: 9.0419 Evaluate side-chains 76 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133866 restraints weight = 8483.113| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.53 r_work: 0.3258 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7746 Z= 0.197 Angle : 0.561 8.623 10500 Z= 0.291 Chirality : 0.045 0.150 1188 Planarity : 0.004 0.033 1394 Dihedral : 5.197 37.370 1062 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.34 % Allowed : 12.93 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.27), residues: 982 helix: -0.63 (0.28), residues: 386 sheet: -1.94 (0.46), residues: 134 loop : -2.07 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.013 0.001 TYR D 66 PHE 0.012 0.002 PHE A 248 TRP 0.007 0.001 TRP A 273 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 7746) covalent geometry : angle 0.56077 (10500) hydrogen bonds : bond 0.03554 ( 280) hydrogen bonds : angle 3.84704 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7552 (tp30) REVERT: B 78 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7569 (tp30) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.0819 time to fit residues: 9.4754 Evaluate side-chains 80 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.0060 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.183941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133794 restraints weight = 8437.106| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.53 r_work: 0.3248 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7746 Z= 0.142 Angle : 0.517 8.461 10500 Z= 0.269 Chirality : 0.043 0.147 1188 Planarity : 0.003 0.032 1394 Dihedral : 4.988 35.348 1062 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.97 % Allowed : 14.29 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.27), residues: 982 helix: -0.47 (0.28), residues: 386 sheet: -1.96 (0.46), residues: 134 loop : -1.96 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.012 0.001 TYR C 66 PHE 0.011 0.001 PHE B 248 TRP 0.006 0.001 TRP A 273 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7746) covalent geometry : angle 0.51712 (10500) hydrogen bonds : bond 0.03064 ( 280) hydrogen bonds : angle 3.67889 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7580 (tp30) REVERT: B 78 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7597 (tp30) REVERT: D 46 GLU cc_start: 0.6588 (pm20) cc_final: 0.6279 (pm20) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.0773 time to fit residues: 8.9995 Evaluate side-chains 79 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 87 optimal weight: 0.0970 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.191205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141731 restraints weight = 8394.285| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.52 r_work: 0.3352 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7746 Z= 0.082 Angle : 0.470 8.349 10500 Z= 0.243 Chirality : 0.042 0.153 1188 Planarity : 0.003 0.029 1394 Dihedral : 4.446 29.112 1062 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.22 % Allowed : 13.67 % Favored : 84.11 % 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: -1.64 (0.27), residues: 982 helix: 0.04 (0.28), residues: 386 sheet: -1.71 (0.42), residues: 158 loop : -1.83 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.009 0.001 TYR C 66 PHE 0.008 0.001 PHE B 248 TRP 0.005 0.001 TRP A 273 HIS 0.002 0.000 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 7746) covalent geometry : angle 0.46957 (10500) hydrogen bonds : bond 0.02138 ( 280) hydrogen bonds : angle 3.27412 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7625 (tp30) REVERT: B 78 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7617 (tp30) REVERT: D 46 GLU cc_start: 0.6461 (pm20) cc_final: 0.6191 (pm20) outliers start: 18 outliers final: 16 residues processed: 96 average time/residue: 0.0921 time to fit residues: 12.1610 Evaluate side-chains 88 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 32 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134839 restraints weight = 8522.600| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.71 r_work: 0.3250 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7746 Z= 0.182 Angle : 0.540 8.360 10500 Z= 0.280 Chirality : 0.044 0.141 1188 Planarity : 0.003 0.032 1394 Dihedral : 4.854 32.481 1062 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.09 % Allowed : 14.29 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.69 (0.27), residues: 982 helix: -0.03 (0.28), residues: 386 sheet: -1.73 (0.43), residues: 158 loop : -1.84 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.012 0.001 TYR C 66 PHE 0.011 0.002 PHE B 248 TRP 0.005 0.001 TRP B 273 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7746) covalent geometry : angle 0.54005 (10500) hydrogen bonds : bond 0.03346 ( 280) hydrogen bonds : angle 3.69017 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7571 (tp30) REVERT: B 78 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7587 (tp30) REVERT: D 46 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6247 (pm20) outliers start: 17 outliers final: 15 residues processed: 81 average time/residue: 0.0826 time to fit residues: 9.4638 Evaluate side-chains 82 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.187534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138048 restraints weight = 8432.260| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.49 r_work: 0.3286 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7746 Z= 0.101 Angle : 0.484 8.341 10500 Z= 0.251 Chirality : 0.042 0.146 1188 Planarity : 0.003 0.030 1394 Dihedral : 4.599 30.631 1062 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.72 % Allowed : 14.66 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.45 (0.28), residues: 982 helix: 0.28 (0.28), residues: 384 sheet: -1.61 (0.43), residues: 158 loop : -1.81 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.010 0.001 TYR C 66 PHE 0.010 0.001 PHE B 248 TRP 0.005 0.001 TRP A 273 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7746) covalent geometry : angle 0.48448 (10500) hydrogen bonds : bond 0.02585 ( 280) hydrogen bonds : angle 3.43147 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7627 (tp30) REVERT: B 78 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7625 (tp30) REVERT: D 46 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6151 (pm20) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.0816 time to fit residues: 9.5215 Evaluate side-chains 84 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.0470 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.190111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140848 restraints weight = 8470.871| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.60 r_work: 0.3349 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7746 Z= 0.091 Angle : 0.473 8.345 10500 Z= 0.243 Chirality : 0.042 0.147 1188 Planarity : 0.003 0.029 1394 Dihedral : 4.417 28.861 1062 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.72 % Allowed : 14.41 % Favored : 83.87 % 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: -1.21 (0.28), residues: 982 helix: 0.56 (0.29), residues: 384 sheet: -1.47 (0.44), residues: 158 loop : -1.76 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.009 0.001 TYR C 66 PHE 0.008 0.001 PHE B 248 TRP 0.003 0.001 TRP B 273 HIS 0.002 0.000 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 7746) covalent geometry : angle 0.47291 (10500) hydrogen bonds : bond 0.02372 ( 280) hydrogen bonds : angle 3.29704 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1735.61 seconds wall clock time: 30 minutes 19.54 seconds (1819.54 seconds total)