Starting phenix.real_space_refine on Tue Mar 3 18:16:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7szi_25567/03_2026/7szi_25567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7szi_25567/03_2026/7szi_25567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7szi_25567/03_2026/7szi_25567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7szi_25567/03_2026/7szi_25567.map" model { file = "/net/cci-nas-00/data/ceres_data/7szi_25567/03_2026/7szi_25567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7szi_25567/03_2026/7szi_25567.cif" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.025 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: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 5058 2.51 5 N 1361 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 8089 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2695 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2665 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 338} Chain breaks: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 60 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 1.85, per 1000 atoms: 0.23 Number of scatterers: 8089 At special positions: 0 Unit cell: (74.52, 95.04, 96.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1662 8.00 N 1361 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 0 " - pdb=" SG CYS D 8 " distance=2.94 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: 0.73 Conformation dependent library (CDL) restraints added in 345.8 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 7.3% alpha, 48.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.583A pdb=" N GLN C 172 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 322 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1 through 6 current: chain 'A' and resid 51 through 61 removed outlier: 6.331A pdb=" N ASN A 59 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR A 74 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN A 61 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA A 72 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 88 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 132 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP A 90 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 130 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY A 92 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ASN A 215 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA A 242 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 243 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 250 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ALA A 251 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 283 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG A 270 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 300 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER A 272 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 298 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA A 274 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A 296 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 276 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 294 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 278 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 282 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 15 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1 through 6 current: chain 'B' and resid 50 through 61 removed outlier: 6.339A pdb=" N ASN B 59 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR B 74 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 61 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 72 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 12.668A pdb=" N ARG B 75 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 95 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 88 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 132 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 90 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 130 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 92 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 147 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N ASN B 215 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 242 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 243 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 250 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ALA B 251 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 283 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 280 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B 291 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP B 282 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 289 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1 through 6 current: chain 'C' and resid 50 through 61 removed outlier: 6.530A pdb=" N THR C 51 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 81 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 53 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA C 79 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN C 55 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 77 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 88 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR C 132 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 90 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA C 130 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY C 92 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N ASN C 215 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 242 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR C 231 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR C 263 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA C 233 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA C 261 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN C 235 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 259 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR C 237 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE C 257 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR C 239 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 255 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C 241 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS C 253 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C 243 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N ALA C 251 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU C 283 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY C 280 " --> pdb=" O ASP C 291 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP C 291 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP C 282 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP C 289 " --> pdb=" O ASP C 282 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1020 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: 1.19 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2729 1.34 - 1.46: 2197 1.46 - 1.58: 3323 1.58 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 8263 Sorted by residual: bond pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.06e-02 8.90e+03 7.19e-01 bond pdb=" C TYR A 116 " pdb=" N GLY A 117 " ideal model delta sigma weight residual 1.336 1.328 0.008 1.01e-02 9.80e+03 6.36e-01 bond pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.29e-02 6.01e+03 4.90e-01 bond pdb=" CA PHE A 83 " pdb=" CB PHE A 83 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.30e-02 5.92e+03 4.31e-01 bond pdb=" N GLY A 221 " pdb=" CA GLY A 221 " ideal model delta sigma weight residual 1.454 1.448 0.006 9.90e-03 1.02e+04 3.81e-01 ... (remaining 8258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 10571 0.88 - 1.76: 520 1.76 - 2.64: 66 2.64 - 3.53: 19 3.53 - 4.41: 9 Bond angle restraints: 11185 Sorted by residual: angle pdb=" C TYR A 116 " pdb=" N GLY A 117 " pdb=" CA GLY A 117 " ideal model delta sigma weight residual 122.47 120.21 2.26 8.90e-01 1.26e+00 6.47e+00 angle pdb=" C GLY D 3 " pdb=" N GLN D 4 " pdb=" CA GLN D 4 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.32e+00 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N GLY A 222 " ideal model delta sigma weight residual 115.49 117.81 -2.32 1.03e+00 9.43e-01 5.09e+00 angle pdb=" CA TYR B 58 " pdb=" CB TYR B 58 " pdb=" CG TYR B 58 " ideal model delta sigma weight residual 113.90 117.79 -3.89 1.80e+00 3.09e-01 4.67e+00 angle pdb=" C TYR B 116 " pdb=" N GLY B 117 " pdb=" CA GLY B 117 " ideal model delta sigma weight residual 122.69 120.38 2.31 1.08e+00 8.57e-01 4.58e+00 ... (remaining 11180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 4222 15.35 - 30.70: 352 30.70 - 46.06: 75 46.06 - 61.41: 37 61.41 - 76.76: 5 Dihedral angle restraints: 4691 sinusoidal: 1765 harmonic: 2926 Sorted by residual: dihedral pdb=" CB CYS D 0 " pdb=" SG CYS D 0 " pdb=" SG CYS D 8 " pdb=" CB CYS D 8 " ideal model delta sinusoidal sigma weight residual 93.00 152.84 -59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " pdb=" CD LYS C 153 " pdb=" CE LYS C 153 " ideal model delta sinusoidal sigma weight residual 60.00 111.18 -51.18 3 1.50e+01 4.44e-03 8.98e+00 dihedral pdb=" CG LYS A 171 " pdb=" CD LYS A 171 " pdb=" CE LYS A 171 " pdb=" NZ LYS A 171 " ideal model delta sinusoidal sigma weight residual -60.00 -110.97 50.97 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 4688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 626 0.026 - 0.052: 343 0.052 - 0.078: 98 0.078 - 0.105: 40 0.105 - 0.131: 26 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1130 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 58 " -0.018 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR B 58 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 58 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 58 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 58 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 58 " 0.014 2.00e-02 2.50e+03 8.94e-03 1.60e+00 pdb=" CG TYR C 58 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 58 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 58 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 207 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 208 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.015 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2113 2.79 - 3.32: 6730 3.32 - 3.85: 13116 3.85 - 4.37: 16407 4.37 - 4.90: 29830 Nonbonded interactions: 68196 Sorted by model distance: nonbonded pdb=" OH TYR B 22 " pdb=" OE2 GLU B 110 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 22 " pdb=" OE2 GLU A 110 " model vdw 2.303 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASN B 127 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR C 105 " pdb=" OE2 GLU C 258 " model vdw 2.317 3.040 nonbonded pdb=" ND2 ASN A 252 " pdb=" OE2 GLU A 284 " model vdw 2.328 3.120 ... (remaining 68191 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 0 through 184 or resid 189 through 344)) selection = (chain 'B' and (resid 0 through 184 or resid 189 through 344)) selection = (chain 'C' and (resid 0 through 184 or resid 189 through 344)) } 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: 1.100 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.010 0.909 8264 Z= 0.514 Angle : 0.478 19.139 11187 Z= 0.273 Chirality : 0.038 0.131 1133 Planarity : 0.002 0.026 1505 Dihedral : 13.000 76.760 2878 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1026 helix: -0.12 (0.84), residues: 37 sheet: 1.39 (0.22), residues: 510 loop : -1.07 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 125 TYR 0.026 0.001 TYR B 58 PHE 0.013 0.001 PHE A 137 TRP 0.016 0.001 TRP B 186 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8263) covalent geometry : angle 0.44087 (11185) SS BOND : bond 0.90891 ( 1) SS BOND : angle 13.89376 ( 2) hydrogen bonds : bond 0.20696 ( 366) hydrogen bonds : angle 8.93980 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.237 Fit side-chains REVERT: A 160 GLU cc_start: 0.8426 (tp30) cc_final: 0.8151 (tm-30) REVERT: A 235 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8565 (pp30) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.7834 time to fit residues: 47.5434 Evaluate side-chains 52 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.070812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.058743 restraints weight = 15489.174| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.50 r_work: 0.2517 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8264 Z= 0.208 Angle : 0.537 6.362 11187 Z= 0.303 Chirality : 0.042 0.173 1133 Planarity : 0.003 0.032 1505 Dihedral : 4.533 45.536 1158 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 0.48 % Allowed : 4.70 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1026 helix: 0.68 (0.92), residues: 37 sheet: 1.27 (0.22), residues: 532 loop : -0.98 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 167 TYR 0.026 0.001 TYR B 58 PHE 0.015 0.001 PHE A 137 TRP 0.010 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8263) covalent geometry : angle 0.53632 (11185) SS BOND : bond 0.00811 ( 1) SS BOND : angle 1.66405 ( 2) hydrogen bonds : bond 0.04262 ( 366) hydrogen bonds : angle 6.32978 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.312 Fit side-chains REVERT: A 160 GLU cc_start: 0.9109 (tp30) cc_final: 0.8696 (tm-30) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.7876 time to fit residues: 44.6363 Evaluate side-chains 51 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.073258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.061216 restraints weight = 15119.637| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.49 r_work: 0.2566 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8264 Z= 0.104 Angle : 0.461 4.484 11187 Z= 0.263 Chirality : 0.039 0.174 1133 Planarity : 0.003 0.037 1505 Dihedral : 4.012 23.240 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.30 % Rotamer: Outliers : 0.60 % Allowed : 6.02 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1026 helix: 0.44 (0.86), residues: 43 sheet: 1.31 (0.22), residues: 519 loop : -1.03 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 285 TYR 0.016 0.001 TYR B 58 PHE 0.012 0.001 PHE B 146 TRP 0.008 0.001 TRP C 73 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8263) covalent geometry : angle 0.46125 (11185) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.14237 ( 2) hydrogen bonds : bond 0.03323 ( 366) hydrogen bonds : angle 5.66545 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.308 Fit side-chains REVERT: C 344 PHE cc_start: 0.8774 (p90) cc_final: 0.8523 (p90) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.7376 time to fit residues: 44.2637 Evaluate side-chains 52 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 43 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.2819 r_free = 0.2819 target = 0.068986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.056957 restraints weight = 15734.233| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 2.48 r_work: 0.2485 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 8264 Z= 0.341 Angle : 0.589 5.292 11187 Z= 0.328 Chirality : 0.045 0.177 1133 Planarity : 0.004 0.052 1505 Dihedral : 4.591 32.039 1155 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.45 % Allowed : 7.83 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1026 helix: 0.41 (0.86), residues: 43 sheet: 0.99 (0.21), residues: 554 loop : -1.06 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.028 0.002 TYR B 58 PHE 0.013 0.002 PHE B 137 TRP 0.013 0.002 TRP A 56 HIS 0.009 0.003 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00791 ( 8263) covalent geometry : angle 0.58859 (11185) SS BOND : bond 0.00216 ( 1) SS BOND : angle 1.13843 ( 2) hydrogen bonds : bond 0.04171 ( 366) hydrogen bonds : angle 6.00793 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.299 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.7685 time to fit residues: 44.5062 Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.2864 r_free = 0.2864 target = 0.071377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.059310 restraints weight = 15327.707| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 2.48 r_work: 0.2530 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8264 Z= 0.154 Angle : 0.488 4.919 11187 Z= 0.277 Chirality : 0.040 0.173 1133 Planarity : 0.003 0.048 1505 Dihedral : 4.277 29.205 1155 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.72 % Allowed : 10.12 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1026 helix: 0.45 (0.88), residues: 43 sheet: 1.04 (0.21), residues: 540 loop : -1.11 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 285 TYR 0.018 0.001 TYR B 58 PHE 0.018 0.001 PHE A 344 TRP 0.008 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8263) covalent geometry : angle 0.48837 (11185) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.87403 ( 2) hydrogen bonds : bond 0.03369 ( 366) hydrogen bonds : angle 5.61461 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.318 Fit side-chains REVERT: C 344 PHE cc_start: 0.8888 (p90) cc_final: 0.8646 (p90) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.7499 time to fit residues: 43.3614 Evaluate side-chains 52 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 = 0.2854 r_free = 0.2854 target = 0.070845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.058875 restraints weight = 15369.907| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 2.46 r_work: 0.2523 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8264 Z= 0.181 Angle : 0.497 4.888 11187 Z= 0.281 Chirality : 0.041 0.173 1133 Planarity : 0.003 0.049 1505 Dihedral : 4.286 28.406 1155 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.20 % Allowed : 10.12 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1026 helix: 0.41 (0.87), residues: 43 sheet: 0.98 (0.21), residues: 557 loop : -1.09 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 167 TYR 0.019 0.001 TYR B 58 PHE 0.020 0.001 PHE A 344 TRP 0.009 0.001 TRP A 56 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8263) covalent geometry : angle 0.49704 (11185) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.81540 ( 2) hydrogen bonds : bond 0.03424 ( 366) hydrogen bonds : angle 5.61308 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.321 Fit side-chains REVERT: A 258 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8496 (mt-10) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.7605 time to fit residues: 44.7815 Evaluate side-chains 60 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.2865 r_free = 0.2865 target = 0.072451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.059592 restraints weight = 14399.608| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 2.52 r_work: 0.2494 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2365 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8264 Z= 0.197 Angle : 0.509 4.849 11187 Z= 0.287 Chirality : 0.041 0.176 1133 Planarity : 0.003 0.051 1505 Dihedral : 4.319 27.744 1155 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 1.08 % Allowed : 10.48 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1026 helix: 0.29 (0.86), residues: 43 sheet: 0.95 (0.21), residues: 557 loop : -1.13 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 285 TYR 0.019 0.001 TYR B 58 PHE 0.021 0.001 PHE A 344 TRP 0.009 0.001 TRP A 56 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8263) covalent geometry : angle 0.50907 (11185) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.76689 ( 2) hydrogen bonds : bond 0.03473 ( 366) hydrogen bonds : angle 5.62549 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.281 Fit side-chains REVERT: A 258 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8624 (mt-10) outliers start: 9 outliers final: 9 residues processed: 54 average time/residue: 0.7199 time to fit residues: 40.9544 Evaluate side-chains 59 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.2881 r_free = 0.2881 target = 0.073230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.060425 restraints weight = 14215.619| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 2.50 r_work: 0.2514 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8264 Z= 0.149 Angle : 0.482 4.551 11187 Z= 0.274 Chirality : 0.040 0.170 1133 Planarity : 0.003 0.048 1505 Dihedral : 4.171 24.930 1155 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.08 % Allowed : 10.84 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1026 helix: 0.25 (0.86), residues: 43 sheet: 0.96 (0.21), residues: 554 loop : -1.11 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 285 TYR 0.016 0.001 TYR B 58 PHE 0.020 0.001 PHE A 344 TRP 0.008 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8263) covalent geometry : angle 0.48209 (11185) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.68992 ( 2) hydrogen bonds : bond 0.03214 ( 366) hydrogen bonds : angle 5.47991 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.313 Fit side-chains REVERT: A 258 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 285 ARG cc_start: 0.8912 (mmt-90) cc_final: 0.8659 (mmt-90) outliers start: 9 outliers final: 9 residues processed: 57 average time/residue: 0.7369 time to fit residues: 44.2162 Evaluate side-chains 61 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.2843 r_free = 0.2843 target = 0.071163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.058371 restraints weight = 14516.887| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 2.50 r_work: 0.2469 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2339 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8264 Z= 0.285 Angle : 0.558 5.026 11187 Z= 0.312 Chirality : 0.043 0.174 1133 Planarity : 0.003 0.057 1505 Dihedral : 4.481 28.506 1155 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 0.84 % Allowed : 11.33 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1026 helix: 0.24 (0.86), residues: 43 sheet: 0.89 (0.21), residues: 555 loop : -1.20 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.023 0.002 TYR B 58 PHE 0.020 0.002 PHE A 344 TRP 0.012 0.002 TRP A 56 HIS 0.007 0.002 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 8263) covalent geometry : angle 0.55837 (11185) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.82613 ( 2) hydrogen bonds : bond 0.03783 ( 366) hydrogen bonds : angle 5.77601 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.308 Fit side-chains REVERT: A 258 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8576 (mt-10) REVERT: C 285 ARG cc_start: 0.8983 (mmt-90) cc_final: 0.8703 (mmt-90) outliers start: 7 outliers final: 8 residues processed: 52 average time/residue: 0.7520 time to fit residues: 41.1244 Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.2904 r_free = 0.2904 target = 0.074538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.061771 restraints weight = 14278.140| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.48 r_work: 0.2543 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8264 Z= 0.105 Angle : 0.465 4.499 11187 Z= 0.265 Chirality : 0.039 0.171 1133 Planarity : 0.003 0.047 1505 Dihedral : 4.046 22.639 1155 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.72 % Allowed : 11.57 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1026 helix: 0.19 (0.86), residues: 43 sheet: 1.02 (0.21), residues: 537 loop : -1.18 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 125 TYR 0.011 0.001 TYR B 58 PHE 0.020 0.001 PHE A 344 TRP 0.009 0.001 TRP C 73 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8263) covalent geometry : angle 0.46471 (11185) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.59715 ( 2) hydrogen bonds : bond 0.02953 ( 366) hydrogen bonds : angle 5.34030 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.244 Fit side-chains REVERT: A 57 GLU cc_start: 0.9162 (tt0) cc_final: 0.8926 (tt0) REVERT: A 258 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8525 (mt-10) REVERT: C 285 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8686 (mmt-90) REVERT: C 344 PHE cc_start: 0.8829 (p90) cc_final: 0.8612 (p90) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.7878 time to fit residues: 44.7302 Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.2865 r_free = 0.2865 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.059833 restraints weight = 14314.108| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.47 r_work: 0.2489 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2360 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8264 Z= 0.212 Angle : 0.525 4.788 11187 Z= 0.294 Chirality : 0.042 0.187 1133 Planarity : 0.003 0.052 1505 Dihedral : 4.334 25.715 1155 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 0.60 % Allowed : 11.81 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1026 helix: 0.24 (0.87), residues: 43 sheet: 0.92 (0.21), residues: 557 loop : -1.15 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 285 TYR 0.020 0.001 TYR B 58 PHE 0.024 0.002 PHE A 138 TRP 0.012 0.001 TRP A 56 HIS 0.006 0.002 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8263) covalent geometry : angle 0.52469 (11185) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.69924 ( 2) hydrogen bonds : bond 0.03487 ( 366) hydrogen bonds : angle 5.60331 ( 1020) =============================================================================== Job complete usr+sys time: 2263.32 seconds wall clock time: 39 minutes 24.07 seconds (2364.07 seconds total)