Starting phenix.real_space_refine on Fri Jun 6 15:22:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7szi_25567/06_2025/7szi_25567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7szi_25567/06_2025/7szi_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_25567/06_2025/7szi_25567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7szi_25567/06_2025/7szi_25567.map" model { file = "/net/cci-nas-00/data/ceres_data/7szi_25567/06_2025/7szi_25567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7szi_25567/06_2025/7szi_25567.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.06, per 1000 atoms: 0.63 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: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 2.24 Time building geometry restraints manager: 2.08 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.000 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (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 TRP 0.016 0.001 TRP B 186 HIS 0.002 0.001 HIS B 197 PHE 0.013 0.001 PHE A 137 TYR 0.026 0.001 TYR B 58 ARG 0.002 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.20696 ( 366) hydrogen bonds : angle 8.93980 ( 1020) SS BOND : bond 0.90891 ( 1) SS BOND : angle 13.89376 ( 2) covalent geometry : bond 0.00245 ( 8263) covalent geometry : angle 0.44087 (11185) *********************** 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 : 0.851 Fit side-chains REVERT: A 160 GLU cc_start: 0.8425 (tp30) cc_final: 0.8151 (tm-30) REVERT: A 235 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8566 (pp30) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 1.6384 time to fit residues: 100.2147 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 : 0.939 ------------------------------------------------------------------------------- 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 86 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.0030 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 151 GLN B 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.071917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.059891 restraints weight = 15176.168| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 2.49 r_work: 0.2537 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8264 Z= 0.156 Angle : 0.511 6.562 11187 Z= 0.290 Chirality : 0.041 0.173 1133 Planarity : 0.003 0.029 1505 Dihedral : 4.392 45.095 1158 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.30 % Rotamer: Outliers : 0.60 % Allowed : 4.46 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1026 helix: 0.72 (0.93), residues: 37 sheet: 1.30 (0.22), residues: 532 loop : -0.95 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 56 HIS 0.003 0.001 HIS B 197 PHE 0.015 0.001 PHE A 137 TYR 0.023 0.001 TYR B 58 ARG 0.003 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 366) hydrogen bonds : angle 6.25298 ( 1020) SS BOND : bond 0.01041 ( 1) SS BOND : angle 1.56809 ( 2) covalent geometry : bond 0.00346 ( 8263) covalent geometry : angle 0.51067 (11185) *********************** 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 58 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.871 Fit side-chains REVERT: C 285 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8500 (mmt-90) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 1.6635 time to fit residues: 96.4263 Evaluate side-chains 50 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.2834 r_free = 0.2834 target = 0.069809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.057746 restraints weight = 15582.111| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.50 r_work: 0.2499 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2382 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8264 Z= 0.266 Angle : 0.551 5.564 11187 Z= 0.310 Chirality : 0.043 0.176 1133 Planarity : 0.004 0.046 1505 Dihedral : 4.479 30.737 1155 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 1.08 % Allowed : 5.78 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1026 helix: 0.73 (0.94), residues: 37 sheet: 1.10 (0.21), residues: 553 loop : -1.01 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 56 HIS 0.007 0.002 HIS B 197 PHE 0.014 0.002 PHE C 344 TYR 0.027 0.002 TYR B 58 ARG 0.005 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 366) hydrogen bonds : angle 6.04661 ( 1020) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.32460 ( 2) covalent geometry : bond 0.00613 ( 8263) covalent geometry : angle 0.55104 (11185) *********************** 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 61 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.888 Fit side-chains REVERT: C 285 ARG cc_start: 0.9062 (mmt-90) cc_final: 0.8551 (mmt-90) REVERT: C 344 PHE cc_start: 0.8830 (p90) cc_final: 0.8549 (p90) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 1.5855 time to fit residues: 95.4048 Evaluate side-chains 58 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.070856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.058868 restraints weight = 15313.891| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.45 r_work: 0.2523 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8264 Z= 0.182 Angle : 0.503 4.955 11187 Z= 0.285 Chirality : 0.041 0.174 1133 Planarity : 0.003 0.048 1505 Dihedral : 4.321 29.759 1155 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 0.96 % Allowed : 8.80 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1026 helix: 0.47 (0.87), residues: 43 sheet: 1.04 (0.21), residues: 553 loop : -1.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 56 HIS 0.005 0.001 HIS B 197 PHE 0.018 0.001 PHE A 344 TYR 0.020 0.001 TYR B 58 ARG 0.002 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 366) hydrogen bonds : angle 5.74997 ( 1020) SS BOND : bond 0.00172 ( 1) SS BOND : angle 1.02014 ( 2) covalent geometry : bond 0.00415 ( 8263) covalent geometry : angle 0.50285 (11185) *********************** 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 61 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.901 Fit side-chains REVERT: C 344 PHE cc_start: 0.8918 (p90) cc_final: 0.8660 (p90) outliers start: 8 outliers final: 2 residues processed: 57 average time/residue: 1.5418 time to fit residues: 92.8039 Evaluate side-chains 52 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.2845 r_free = 0.2845 target = 0.071328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.058667 restraints weight = 14283.685| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 2.45 r_work: 0.2477 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8264 Z= 0.265 Angle : 0.544 5.069 11187 Z= 0.306 Chirality : 0.043 0.176 1133 Planarity : 0.003 0.053 1505 Dihedral : 4.509 32.137 1155 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 1.08 % Allowed : 9.88 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1026 helix: 0.70 (0.95), residues: 37 sheet: 0.94 (0.21), residues: 552 loop : -1.15 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 56 HIS 0.007 0.002 HIS B 197 PHE 0.022 0.002 PHE A 344 TYR 0.023 0.002 TYR B 58 ARG 0.002 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 366) hydrogen bonds : angle 5.84400 ( 1020) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.96024 ( 2) covalent geometry : bond 0.00612 ( 8263) covalent geometry : angle 0.54367 (11185) *********************** 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 57 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.964 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 1.4822 time to fit residues: 86.3705 Evaluate side-chains 57 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE 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 49 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.071354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.059360 restraints weight = 15212.621| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.47 r_work: 0.2527 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1321 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= 0.145 Angle : 0.484 4.634 11187 Z= 0.275 Chirality : 0.040 0.173 1133 Planarity : 0.003 0.048 1505 Dihedral : 4.241 28.345 1155 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 0.96 % Allowed : 9.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1026 helix: 0.43 (0.88), residues: 43 sheet: 0.97 (0.21), residues: 555 loop : -1.13 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.004 0.001 HIS B 197 PHE 0.019 0.001 PHE A 344 TYR 0.016 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 366) hydrogen bonds : angle 5.55969 ( 1020) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.77101 ( 2) covalent geometry : bond 0.00328 ( 8263) covalent geometry : angle 0.48378 (11185) *********************** 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 64 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.843 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 1.5224 time to fit residues: 99.6518 Evaluate side-chains 60 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 30 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.2892 r_free = 0.2892 target = 0.072853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.060787 restraints weight = 15211.488| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.47 r_work: 0.2561 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1442 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= 0.107 Angle : 0.459 4.511 11187 Z= 0.261 Chirality : 0.040 0.172 1133 Planarity : 0.003 0.046 1505 Dihedral : 4.005 22.783 1155 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.84 % Allowed : 10.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1026 helix: 0.28 (0.86), residues: 43 sheet: 1.00 (0.21), residues: 547 loop : -1.10 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS B 197 PHE 0.018 0.001 PHE A 344 TYR 0.013 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 366) hydrogen bonds : angle 5.31713 ( 1020) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.66086 ( 2) covalent geometry : bond 0.00234 ( 8263) covalent geometry : angle 0.45854 (11185) *********************** 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 61 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.941 Fit side-chains REVERT: B 179 THR cc_start: 0.9115 (p) cc_final: 0.8895 (t) REVERT: C 285 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8434 (mmt-90) REVERT: C 344 PHE cc_start: 0.8815 (p90) cc_final: 0.8590 (p90) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 1.4861 time to fit residues: 92.6542 Evaluate side-chains 54 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 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 = 0.2855 r_free = 0.2855 target = 0.071902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.059076 restraints weight = 14505.183| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 2.51 r_work: 0.2484 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2356 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8264 Z= 0.244 Angle : 0.531 4.854 11187 Z= 0.298 Chirality : 0.042 0.176 1133 Planarity : 0.003 0.051 1505 Dihedral : 4.374 26.976 1155 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 0.96 % Allowed : 10.84 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1026 helix: 0.31 (0.87), residues: 43 sheet: 0.91 (0.21), residues: 557 loop : -1.15 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 56 HIS 0.006 0.002 HIS B 197 PHE 0.022 0.002 PHE A 344 TYR 0.021 0.001 TYR B 58 ARG 0.002 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 366) hydrogen bonds : angle 5.66600 ( 1020) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.72944 ( 2) covalent geometry : bond 0.00565 ( 8263) covalent geometry : angle 0.53130 (11185) *********************** 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 58 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.968 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 1.6037 time to fit residues: 91.5047 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.2861 r_free = 0.2861 target = 0.072241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.059476 restraints weight = 14535.582| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.49 r_work: 0.2495 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2366 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1422 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= 0.205 Angle : 0.515 4.759 11187 Z= 0.290 Chirality : 0.041 0.173 1133 Planarity : 0.003 0.050 1505 Dihedral : 4.325 26.214 1155 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 0.84 % Allowed : 11.20 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1026 helix: 0.27 (0.87), residues: 43 sheet: 0.90 (0.21), residues: 557 loop : -1.18 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.005 0.002 HIS B 197 PHE 0.022 0.001 PHE A 344 TYR 0.019 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 366) hydrogen bonds : angle 5.60460 ( 1020) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.72108 ( 2) covalent geometry : bond 0.00473 ( 8263) covalent geometry : angle 0.51450 (11185) *********************** 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 54 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.883 Fit side-chains REVERT: C 285 ARG cc_start: 0.8920 (mmt-90) cc_final: 0.8667 (mmt-90) outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 1.6015 time to fit residues: 84.6002 Evaluate side-chains 54 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.2871 r_free = 0.2871 target = 0.072769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.060015 restraints weight = 14222.570| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.49 r_work: 0.2506 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1433 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= 0.173 Angle : 0.500 4.578 11187 Z= 0.282 Chirality : 0.041 0.173 1133 Planarity : 0.003 0.048 1505 Dihedral : 4.245 24.939 1155 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1026 helix: 0.27 (0.87), residues: 43 sheet: 0.90 (0.21), residues: 557 loop : -1.14 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 PHE 0.020 0.001 PHE A 344 TYR 0.017 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 366) hydrogen bonds : angle 5.52799 ( 1020) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.68482 ( 2) covalent geometry : bond 0.00395 ( 8263) covalent geometry : angle 0.49991 (11185) ********************** 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 57 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.941 Fit side-chains REVERT: C 285 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8700 (mmt-90) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 1.6031 time to fit residues: 91.4433 Evaluate side-chains 57 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.2849 r_free = 0.2849 target = 0.071518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.058771 restraints weight = 14545.735| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 2.49 r_work: 0.2482 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2353 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8264 Z= 0.248 Angle : 0.544 5.136 11187 Z= 0.304 Chirality : 0.042 0.173 1133 Planarity : 0.003 0.052 1505 Dihedral : 4.431 27.309 1155 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 0.72 % Allowed : 11.33 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1026 helix: 0.24 (0.86), residues: 43 sheet: 0.87 (0.21), residues: 556 loop : -1.20 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 56 HIS 0.007 0.002 HIS B 197 PHE 0.022 0.002 PHE A 344 TYR 0.021 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 366) hydrogen bonds : angle 5.69694 ( 1020) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.76498 ( 2) covalent geometry : bond 0.00573 ( 8263) covalent geometry : angle 0.54430 (11185) =============================================================================== Job complete usr+sys time: 4911.99 seconds wall clock time: 85 minutes 4.54 seconds (5104.54 seconds total)