Starting phenix.real_space_refine on Fri Jul 3 06:47:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vs6_43489/07_2026/8vs6_43489_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vs6_43489/07_2026/8vs6_43489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vs6_43489/07_2026/8vs6_43489_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vs6_43489/07_2026/8vs6_43489_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vs6_43489/07_2026/8vs6_43489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vs6_43489/07_2026/8vs6_43489.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.097 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 31 5.16 5 C 4055 2.51 5 N 1074 2.21 5 O 1272 1.98 5 H 6015 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12453 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 163 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "A" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 6588 Classifications: {'peptide': 441} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5470 Classifications: {'peptide': 349} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.90, per 1000 atoms: 0.15 Number of scatterers: 12453 At special positions: 0 Unit cell: (72.63, 102.22, 95.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 S 31 16.00 Mg 1 11.99 O 1272 8.00 N 1074 7.00 C 4055 6.00 H 6015 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1101 " - " ASN A 260 " " NAG B 701 " - " ASN B 360 " " NAG B 702 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 191 " " NAG G 1 " - " ASN B 389 " " NAG H 1 " - " ASN B 414 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 310.3 milliseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 18.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.253A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.622A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.685A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.589A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.663A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.768A pdb=" N SER B 275 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.526A pdb=" N TYR B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 344 removed outlier: 3.658A pdb=" N VAL B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.352A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 411 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.911A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.661A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.044A pdb=" N LYS A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.678A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.563A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.886A pdb=" N ASP A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.462A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 85 Processing sheet with id=AB4, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.392A pdb=" N PHE B 146 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER B 187 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU B 144 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR B 189 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE B 142 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 237 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 345 through 346 206 hydrogen bonds defined for protein. 525 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: 2.25 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6015 1.03 - 1.23: 14 1.23 - 1.42: 2759 1.42 - 1.62: 3748 1.62 - 1.81: 48 Bond restraints: 12584 Sorted by residual: bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" N GLY E 240 " pdb=" CA GLY E 240 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.04e+00 bond pdb=" C3 BMA C 3 " pdb=" O3 BMA C 3 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.410 1.446 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 1.407 1.442 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 12579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 22011 1.70 - 3.40: 498 3.40 - 5.10: 65 5.10 - 6.80: 7 6.80 - 8.49: 2 Bond angle restraints: 22583 Sorted by residual: angle pdb=" CB GLN B 353 " pdb=" CG GLN B 353 " pdb=" CD GLN B 353 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.70e+00 3.46e-01 8.81e+00 angle pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " pdb=" C5 BMA C 3 " ideal model delta sigma weight residual 118.82 110.33 8.49 3.00e+00 1.11e-01 8.02e+00 angle pdb=" N VAL A 312 " pdb=" CA VAL A 312 " pdb=" C VAL A 312 " ideal model delta sigma weight residual 113.42 110.29 3.13 1.17e+00 7.31e-01 7.18e+00 angle pdb=" N ASP A 148 " pdb=" CA ASP A 148 " pdb=" C ASP A 148 " ideal model delta sigma weight residual 107.73 104.23 3.50 1.34e+00 5.57e-01 6.82e+00 angle pdb=" C3 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 111.77 104.42 7.35 3.00e+00 1.11e-01 6.01e+00 ... (remaining 22578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.85: 5608 20.85 - 41.71: 426 41.71 - 62.56: 148 62.56 - 83.42: 26 83.42 - 104.27: 12 Dihedral angle restraints: 6220 sinusoidal: 3507 harmonic: 2713 Sorted by residual: dihedral pdb=" CA ASP A 353 " pdb=" C ASP A 353 " pdb=" N GLY A 354 " pdb=" CA GLY A 354 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 29 " pdb=" C SER A 29 " pdb=" N ALA A 30 " pdb=" CA ALA A 30 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 60.65 32.35 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 6217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 797 0.052 - 0.103: 145 0.103 - 0.154: 62 0.154 - 0.206: 2 0.206 - 0.257: 2 Chirality restraints: 1008 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.70 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.10e+00 ... (remaining 1005 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 353 " 0.009 2.00e-02 2.50e+03 1.96e-02 5.79e+00 pdb=" CD GLN B 353 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B 353 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 GLN B 353 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 353 " 0.010 2.00e-02 2.50e+03 pdb="HE22 GLN B 353 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 365 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 366 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 419 " 0.012 2.00e-02 2.50e+03 9.08e-03 2.47e+00 pdb=" CG TYR A 419 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 419 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 419 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 419 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 419 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 419 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 419 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 419 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 419 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 419 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 419 " -0.000 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1016 2.22 - 2.81: 25880 2.81 - 3.41: 33810 3.41 - 4.00: 48350 4.00 - 4.60: 72235 Nonbonded interactions: 181291 Sorted by model distance: nonbonded pdb=" O ASN A 2 " pdb=" H ARG A 438 " model vdw 1.622 2.450 nonbonded pdb=" O PHE B 299 " pdb=" H GLY B 322 " model vdw 1.631 2.450 nonbonded pdb="HH11 ARG A 115 " pdb=" O THR A 116 " model vdw 1.647 2.450 nonbonded pdb=" H ASP A 257 " pdb=" O SER A 262 " model vdw 1.659 2.450 nonbonded pdb=" HZ3 LYS A 104 " pdb=" OD1 ASP A 167 " model vdw 1.679 2.450 ... (remaining 181286 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 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.640 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.004 0.059 6593 Z= 0.206 Angle : 0.764 13.007 8957 Z= 0.383 Chirality : 0.049 0.257 1008 Planarity : 0.004 0.060 1148 Dihedral : 16.491 104.269 2662 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 16.34 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.31 (0.29), residues: 791 helix: -0.58 (0.51), residues: 99 sheet: 0.49 (0.31), residues: 266 loop : -0.51 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 378 TYR 0.025 0.002 TYR A 419 PHE 0.009 0.001 PHE A 88 TRP 0.009 0.002 TRP B 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 ( 6569) covalent geometry : angle 0.73718 / 0.38 ( 8892) SS BOND : bond 0.00195 / 0.10 ( 7) SS BOND : angle 0.39306 / 0.30 ( 14) hydrogen bonds : bond 0.20038 / 12.83 ( 206) hydrogen bonds : angle 8.98055 / 6.25 ( 525) link_ALPHA1-2 : bond 0.00884 / 0.55 ( 1) link_ALPHA1-2 : angle 2.58010 / 1.06 ( 3) link_ALPHA1-3 : bond 0.01496 / 0.93 ( 1) link_ALPHA1-3 : angle 1.49691 / 0.57 ( 3) link_ALPHA1-6 : bond 0.00666 / 0.42 ( 1) link_ALPHA1-6 : angle 1.73415 / 0.87 ( 3) link_BETA1-4 : bond 0.01200 / 0.69 ( 6) link_BETA1-4 : angle 3.92514 / 3.32 ( 18) link_NAG-ASN : bond 0.00316 / 0.21 ( 8) link_NAG-ASN : angle 1.86156 / 1.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8415 (m-80) cc_final: 0.7898 (m-80) outliers start: 11 outliers final: 12 residues processed: 85 average time/residue: 0.9615 time to fit residues: 86.6272 Evaluate side-chains 78 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 352 GLN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141864 restraints weight = 19583.023| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.60 r_work: 0.3604 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6593 Z= 0.202 Angle : 0.656 11.152 8957 Z= 0.339 Chirality : 0.049 0.230 1008 Planarity : 0.005 0.055 1148 Dihedral : 9.587 83.178 1228 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.55 % Allowed : 15.29 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.57 (0.29), residues: 791 helix: -0.83 (0.50), residues: 106 sheet: 0.28 (0.30), residues: 263 loop : -0.61 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.023 0.002 TYR A 275 PHE 0.012 0.002 PHE A 217 TRP 0.012 0.002 TRP B 230 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 6569) covalent geometry : angle 0.63111 / 0.33 ( 8892) SS BOND : bond 0.00383 / 0.20 ( 7) SS BOND : angle 0.81929 / 0.47 ( 14) hydrogen bonds : bond 0.04736 / 3.00 ( 206) hydrogen bonds : angle 7.47957 / 5.12 ( 525) link_ALPHA1-2 : bond 0.00302 / 0.19 ( 1) link_ALPHA1-2 : angle 2.20585 / 1.21 ( 3) link_ALPHA1-3 : bond 0.02184 / 1.36 ( 1) link_ALPHA1-3 : angle 2.05631 / 0.75 ( 3) link_ALPHA1-6 : bond 0.00630 / 0.39 ( 1) link_ALPHA1-6 : angle 2.14759 / 1.07 ( 3) link_BETA1-4 : bond 0.01225 / 0.70 ( 6) link_BETA1-4 : angle 3.22813 / 2.88 ( 18) link_NAG-ASN : bond 0.00306 / 0.20 ( 8) link_NAG-ASN : angle 1.77204 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8599 (OUTLIER) cc_final: 0.8298 (p-90) REVERT: A 275 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: A 316 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 369 LYS cc_start: 0.7111 (mtmm) cc_final: 0.6649 (mtpp) REVERT: B 80 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: B 218 MET cc_start: 0.8341 (mtp) cc_final: 0.8082 (ttm) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.9182 time to fit residues: 79.8353 Evaluate side-chains 82 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141704 restraints weight = 19799.379| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.64 r_work: 0.3604 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6593 Z= 0.174 Angle : 0.620 10.361 8957 Z= 0.317 Chirality : 0.048 0.222 1008 Planarity : 0.004 0.044 1148 Dihedral : 8.550 66.167 1220 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.60 % Allowed : 14.84 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.76 (0.28), residues: 791 helix: -0.76 (0.50), residues: 106 sheet: -0.01 (0.30), residues: 263 loop : -0.69 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.023 0.002 TYR A 275 PHE 0.012 0.002 PHE A 19 TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6569) covalent geometry : angle 0.59756 / 0.31 ( 8892) SS BOND : bond 0.00373 / 0.19 ( 7) SS BOND : angle 0.79077 / 0.49 ( 14) hydrogen bonds : bond 0.04080 / 2.58 ( 206) hydrogen bonds : angle 7.04895 / 4.83 ( 525) link_ALPHA1-2 : bond 0.00365 / 0.23 ( 1) link_ALPHA1-2 : angle 1.82969 / 0.98 ( 3) link_ALPHA1-3 : bond 0.02264 / 1.41 ( 1) link_ALPHA1-3 : angle 1.54458 / 0.58 ( 3) link_ALPHA1-6 : bond 0.00785 / 0.49 ( 1) link_ALPHA1-6 : angle 2.13756 / 1.05 ( 3) link_BETA1-4 : bond 0.01127 / 0.64 ( 6) link_BETA1-4 : angle 3.00961 / 2.66 ( 18) link_NAG-ASN : bond 0.00219 / 0.14 ( 8) link_NAG-ASN : angle 1.60759 / 0.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.8206 (p-90) REVERT: A 115 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7711 (ptm160) REVERT: A 275 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7361 (m-10) REVERT: A 329 THR cc_start: 0.8353 (m) cc_final: 0.8004 (t) REVERT: A 369 LYS cc_start: 0.7023 (mtmm) cc_final: 0.6528 (mtpp) REVERT: B 218 MET cc_start: 0.8391 (mtp) cc_final: 0.8159 (ttm) outliers start: 24 outliers final: 13 residues processed: 92 average time/residue: 0.8790 time to fit residues: 85.9544 Evaluate side-chains 89 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 161 HIS B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.162895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140964 restraints weight = 19589.063| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.62 r_work: 0.3597 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6593 Z= 0.198 Angle : 0.633 10.054 8957 Z= 0.322 Chirality : 0.048 0.239 1008 Planarity : 0.005 0.040 1148 Dihedral : 8.173 56.808 1220 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.60 % Allowed : 15.89 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.90 (0.28), residues: 791 helix: -0.74 (0.50), residues: 106 sheet: -0.19 (0.30), residues: 264 loop : -0.74 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.025 0.002 TYR A 275 PHE 0.013 0.002 PHE A 19 TRP 0.012 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 6569) covalent geometry : angle 0.61098 / 0.32 ( 8892) SS BOND : bond 0.00470 / 0.24 ( 7) SS BOND : angle 0.90809 / 0.58 ( 14) hydrogen bonds : bond 0.03763 / 2.40 ( 206) hydrogen bonds : angle 6.94782 / 4.76 ( 525) link_ALPHA1-2 : bond 0.00190 / 0.12 ( 1) link_ALPHA1-2 : angle 1.83637 / 1.00 ( 3) link_ALPHA1-3 : bond 0.02175 / 1.36 ( 1) link_ALPHA1-3 : angle 1.67899 / 0.61 ( 3) link_ALPHA1-6 : bond 0.00707 / 0.44 ( 1) link_ALPHA1-6 : angle 2.06317 / 1.03 ( 3) link_BETA1-4 : bond 0.01139 / 0.64 ( 6) link_BETA1-4 : angle 2.94917 / 2.62 ( 18) link_NAG-ASN : bond 0.00254 / 0.17 ( 8) link_NAG-ASN : angle 1.68649 / 1.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.8265 (p-90) REVERT: A 115 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7821 (ptm160) REVERT: A 275 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7301 (m-10) REVERT: A 329 THR cc_start: 0.8439 (m) cc_final: 0.8062 (t) REVERT: A 369 LYS cc_start: 0.6953 (mtmm) cc_final: 0.6528 (mtpp) REVERT: A 390 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 80 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: B 218 MET cc_start: 0.8416 (mtp) cc_final: 0.8189 (ttm) outliers start: 24 outliers final: 15 residues processed: 90 average time/residue: 0.8662 time to fit residues: 82.7372 Evaluate side-chains 92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 202 GLN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141069 restraints weight = 19719.256| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.62 r_work: 0.3597 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6593 Z= 0.194 Angle : 0.628 9.869 8957 Z= 0.319 Chirality : 0.048 0.235 1008 Planarity : 0.004 0.040 1148 Dihedral : 7.886 50.812 1220 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.90 % Allowed : 16.04 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.97 (0.28), residues: 791 helix: -0.71 (0.51), residues: 106 sheet: -0.30 (0.30), residues: 264 loop : -0.78 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.026 0.002 TYR A 275 PHE 0.013 0.002 PHE A 19 TRP 0.011 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 6569) covalent geometry : angle 0.60710 / 0.32 ( 8892) SS BOND : bond 0.00464 / 0.24 ( 7) SS BOND : angle 0.77872 / 0.48 ( 14) hydrogen bonds : bond 0.03680 / 2.34 ( 206) hydrogen bonds : angle 6.82186 / 4.70 ( 525) link_ALPHA1-2 : bond 0.00287 / 0.18 ( 1) link_ALPHA1-2 : angle 1.80645 / 0.98 ( 3) link_ALPHA1-3 : bond 0.02138 / 1.34 ( 1) link_ALPHA1-3 : angle 1.54947 / 0.58 ( 3) link_ALPHA1-6 : bond 0.00743 / 0.46 ( 1) link_ALPHA1-6 : angle 1.99428 / 1.00 ( 3) link_BETA1-4 : bond 0.01112 / 0.63 ( 6) link_BETA1-4 : angle 2.90824 / 2.58 ( 18) link_NAG-ASN : bond 0.00253 / 0.17 ( 8) link_NAG-ASN : angle 1.66382 / 1.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.8205 (p-90) REVERT: A 115 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7787 (ptm160) REVERT: A 329 THR cc_start: 0.8538 (m) cc_final: 0.8178 (t) REVERT: A 369 LYS cc_start: 0.6990 (mtmm) cc_final: 0.6545 (mtpp) REVERT: A 390 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 430 ASP cc_start: 0.7760 (m-30) cc_final: 0.7536 (m-30) REVERT: B 80 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: B 84 GLN cc_start: 0.6470 (pm20) cc_final: 0.6213 (pm20) REVERT: B 218 MET cc_start: 0.8403 (mtp) cc_final: 0.8180 (ttm) REVERT: B 278 MET cc_start: 0.8515 (ptp) cc_final: 0.7940 (ptp) outliers start: 26 outliers final: 17 residues processed: 93 average time/residue: 0.8498 time to fit residues: 83.9008 Evaluate side-chains 94 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 320 GLN B 202 GLN B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.162659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140775 restraints weight = 19570.873| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.62 r_work: 0.3595 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6593 Z= 0.199 Angle : 0.632 9.695 8957 Z= 0.321 Chirality : 0.048 0.235 1008 Planarity : 0.004 0.041 1148 Dihedral : 7.678 51.756 1220 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.75 % Allowed : 16.49 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.28), residues: 791 helix: -0.75 (0.50), residues: 106 sheet: -0.39 (0.30), residues: 264 loop : -0.80 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.026 0.002 TYR A 275 PHE 0.013 0.002 PHE A 19 TRP 0.012 0.002 TRP B 230 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 6569) covalent geometry : angle 0.61202 / 0.32 ( 8892) SS BOND : bond 0.00414 / 0.21 ( 7) SS BOND : angle 0.80522 / 0.50 ( 14) hydrogen bonds : bond 0.03632 / 2.31 ( 206) hydrogen bonds : angle 6.76211 / 4.66 ( 525) link_ALPHA1-2 : bond 0.00254 / 0.16 ( 1) link_ALPHA1-2 : angle 1.80719 / 0.99 ( 3) link_ALPHA1-3 : bond 0.02131 / 1.33 ( 1) link_ALPHA1-3 : angle 1.51803 / 0.56 ( 3) link_ALPHA1-6 : bond 0.00721 / 0.45 ( 1) link_ALPHA1-6 : angle 1.92298 / 0.99 ( 3) link_BETA1-4 : bond 0.01082 / 0.61 ( 6) link_BETA1-4 : angle 2.86505 / 2.54 ( 18) link_NAG-ASN : bond 0.00269 / 0.19 ( 8) link_NAG-ASN : angle 1.65152 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.8166 (p-90) REVERT: A 329 THR cc_start: 0.8561 (m) cc_final: 0.8215 (t) REVERT: A 369 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6645 (mtpp) REVERT: A 390 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8474 (mp) REVERT: B 84 GLN cc_start: 0.6473 (pm20) cc_final: 0.6077 (pm20) REVERT: B 218 MET cc_start: 0.8367 (mtp) cc_final: 0.8157 (ttm) REVERT: B 278 MET cc_start: 0.8543 (ptp) cc_final: 0.7979 (ptp) outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 0.8510 time to fit residues: 85.1965 Evaluate side-chains 91 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 13 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 152 GLN B 202 GLN B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142090 restraints weight = 19446.028| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.60 r_work: 0.3612 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6593 Z= 0.155 Angle : 0.598 9.410 8957 Z= 0.303 Chirality : 0.047 0.222 1008 Planarity : 0.004 0.038 1148 Dihedral : 7.253 58.335 1218 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.00 % Allowed : 17.54 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.28), residues: 791 helix: -0.63 (0.51), residues: 106 sheet: -0.44 (0.30), residues: 264 loop : -0.78 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.023 0.002 TYR A 275 PHE 0.010 0.002 PHE A 19 TRP 0.010 0.002 TRP B 230 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6569) covalent geometry : angle 0.57889 / 0.30 ( 8892) SS BOND : bond 0.00370 / 0.19 ( 7) SS BOND : angle 0.75742 / 0.47 ( 14) hydrogen bonds : bond 0.03303 / 2.09 ( 206) hydrogen bonds : angle 6.60035 / 4.54 ( 525) link_ALPHA1-2 : bond 0.00356 / 0.22 ( 1) link_ALPHA1-2 : angle 1.74774 / 0.94 ( 3) link_ALPHA1-3 : bond 0.01921 / 1.20 ( 1) link_ALPHA1-3 : angle 1.68920 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00748 / 0.47 ( 1) link_ALPHA1-6 : angle 1.77193 / 0.92 ( 3) link_BETA1-4 : bond 0.01086 / 0.61 ( 6) link_BETA1-4 : angle 2.76332 / 2.44 ( 18) link_NAG-ASN : bond 0.00191 / 0.13 ( 8) link_NAG-ASN : angle 1.46987 / 0.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.8198 (p-90) REVERT: A 329 THR cc_start: 0.8513 (m) cc_final: 0.8208 (t) REVERT: A 369 LYS cc_start: 0.7122 (mtmm) cc_final: 0.6653 (mtpp) REVERT: A 390 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 84 GLN cc_start: 0.6468 (pm20) cc_final: 0.6093 (pm20) REVERT: B 190 GLU cc_start: 0.7012 (tp30) cc_final: 0.6804 (tp30) REVERT: B 218 MET cc_start: 0.8391 (mtp) cc_final: 0.8166 (ttm) REVERT: B 278 MET cc_start: 0.8462 (ptp) cc_final: 0.7888 (ptp) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 0.8137 time to fit residues: 77.9302 Evaluate side-chains 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141465 restraints weight = 19432.484| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.60 r_work: 0.3602 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6593 Z= 0.180 Angle : 0.609 9.320 8957 Z= 0.309 Chirality : 0.048 0.219 1008 Planarity : 0.004 0.039 1148 Dihedral : 7.119 54.716 1218 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.00 % Allowed : 18.14 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.28), residues: 791 helix: -0.63 (0.51), residues: 106 sheet: -0.47 (0.30), residues: 264 loop : -0.77 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.023 0.002 TYR A 275 PHE 0.011 0.002 PHE A 19 TRP 0.011 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 6569) covalent geometry : angle 0.59027 / 0.30 ( 8892) SS BOND : bond 0.00378 / 0.19 ( 7) SS BOND : angle 0.78391 / 0.48 ( 14) hydrogen bonds : bond 0.03439 / 2.17 ( 206) hydrogen bonds : angle 6.59487 / 4.54 ( 525) link_ALPHA1-2 : bond 0.00263 / 0.16 ( 1) link_ALPHA1-2 : angle 1.76829 / 0.96 ( 3) link_ALPHA1-3 : bond 0.02021 / 1.26 ( 1) link_ALPHA1-3 : angle 1.39164 / 0.53 ( 3) link_ALPHA1-6 : bond 0.00744 / 0.46 ( 1) link_ALPHA1-6 : angle 1.80047 / 0.95 ( 3) link_BETA1-4 : bond 0.01066 / 0.60 ( 6) link_BETA1-4 : angle 2.74630 / 2.43 ( 18) link_NAG-ASN : bond 0.00243 / 0.16 ( 8) link_NAG-ASN : angle 1.56453 / 0.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.8176 (p-90) REVERT: A 329 THR cc_start: 0.8596 (m) cc_final: 0.8226 (t) REVERT: A 369 LYS cc_start: 0.7139 (mtmm) cc_final: 0.6659 (mtpp) REVERT: A 390 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8505 (mp) REVERT: B 84 GLN cc_start: 0.6402 (pm20) cc_final: 0.6039 (pm20) REVERT: B 278 MET cc_start: 0.8494 (ptp) cc_final: 0.7914 (ptp) outliers start: 20 outliers final: 15 residues processed: 94 average time/residue: 0.8127 time to fit residues: 81.2537 Evaluate side-chains 93 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 384 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.163704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141813 restraints weight = 19613.144| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.62 r_work: 0.3608 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6593 Z= 0.176 Angle : 0.609 9.168 8957 Z= 0.308 Chirality : 0.047 0.214 1008 Planarity : 0.004 0.038 1148 Dihedral : 6.765 44.163 1214 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.00 % Allowed : 18.44 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.28), residues: 791 helix: -0.62 (0.50), residues: 106 sheet: -0.46 (0.30), residues: 264 loop : -0.76 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.022 0.002 TYR A 275 PHE 0.011 0.002 PHE A 19 TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6569) covalent geometry : angle 0.59114 / 0.30 ( 8892) SS BOND : bond 0.00418 / 0.21 ( 7) SS BOND : angle 0.72826 / 0.45 ( 14) hydrogen bonds : bond 0.03377 / 2.13 ( 206) hydrogen bonds : angle 6.56676 / 4.52 ( 525) link_ALPHA1-2 : bond 0.00285 / 0.18 ( 1) link_ALPHA1-2 : angle 1.77050 / 0.96 ( 3) link_ALPHA1-3 : bond 0.01971 / 1.23 ( 1) link_ALPHA1-3 : angle 1.42732 / 0.54 ( 3) link_ALPHA1-6 : bond 0.00722 / 0.45 ( 1) link_ALPHA1-6 : angle 1.72830 / 0.92 ( 3) link_BETA1-4 : bond 0.01036 / 0.59 ( 6) link_BETA1-4 : angle 2.70529 / 2.39 ( 18) link_NAG-ASN : bond 0.00217 / 0.15 ( 8) link_NAG-ASN : angle 1.52489 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.8196 (p-90) REVERT: A 329 THR cc_start: 0.8603 (m) cc_final: 0.8247 (t) REVERT: A 369 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6665 (mtpp) REVERT: A 390 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 84 GLN cc_start: 0.6431 (pm20) cc_final: 0.6049 (pm20) REVERT: B 278 MET cc_start: 0.8477 (ptp) cc_final: 0.7968 (ptp) outliers start: 20 outliers final: 15 residues processed: 92 average time/residue: 0.7915 time to fit residues: 77.8271 Evaluate side-chains 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 78 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143264 restraints weight = 19503.824| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.62 r_work: 0.3623 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6593 Z= 0.133 Angle : 0.577 8.954 8957 Z= 0.291 Chirality : 0.047 0.199 1008 Planarity : 0.004 0.033 1148 Dihedral : 6.378 43.278 1214 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 19.64 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.95 (0.29), residues: 791 helix: -0.44 (0.51), residues: 106 sheet: -0.41 (0.30), residues: 263 loop : -0.74 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.021 0.001 TYR A 275 PHE 0.010 0.001 PHE A 88 TRP 0.009 0.001 TRP B 230 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6569) covalent geometry : angle 0.55979 / 0.29 ( 8892) SS BOND : bond 0.00352 / 0.18 ( 7) SS BOND : angle 0.72932 / 0.45 ( 14) hydrogen bonds : bond 0.03050 / 1.92 ( 206) hydrogen bonds : angle 6.41673 / 4.42 ( 525) link_ALPHA1-2 : bond 0.00365 / 0.23 ( 1) link_ALPHA1-2 : angle 1.71936 / 0.92 ( 3) link_ALPHA1-3 : bond 0.01731 / 1.08 ( 1) link_ALPHA1-3 : angle 1.58163 / 0.61 ( 3) link_ALPHA1-6 : bond 0.00721 / 0.45 ( 1) link_ALPHA1-6 : angle 1.60413 / 0.87 ( 3) link_BETA1-4 : bond 0.01037 / 0.59 ( 6) link_BETA1-4 : angle 2.61784 / 2.30 ( 18) link_NAG-ASN : bond 0.00159 / 0.11 ( 8) link_NAG-ASN : angle 1.35273 / 0.82 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.8156 (p-90) REVERT: A 329 THR cc_start: 0.8675 (m) cc_final: 0.8352 (t) REVERT: A 369 LYS cc_start: 0.7136 (mtmm) cc_final: 0.6664 (mtpp) REVERT: B 84 GLN cc_start: 0.6433 (pm20) cc_final: 0.6056 (pm20) REVERT: B 278 MET cc_start: 0.8434 (ptp) cc_final: 0.7866 (ptp) REVERT: B 393 THR cc_start: 0.8039 (m) cc_final: 0.7830 (p) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.7647 time to fit residues: 66.7064 Evaluate side-chains 80 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 46 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143067 restraints weight = 19480.516| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.61 r_work: 0.3620 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6593 Z= 0.143 Angle : 0.579 8.840 8957 Z= 0.292 Chirality : 0.047 0.190 1008 Planarity : 0.004 0.034 1148 Dihedral : 6.246 43.740 1213 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.80 % Allowed : 19.94 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.96 (0.28), residues: 791 helix: -0.39 (0.51), residues: 106 sheet: -0.45 (0.30), residues: 264 loop : -0.73 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 236 TYR 0.020 0.001 TYR A 275 PHE 0.009 0.002 PHE A 88 TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6569) covalent geometry : angle 0.56173 / 0.29 ( 8892) SS BOND : bond 0.00383 / 0.19 ( 7) SS BOND : angle 0.73123 / 0.45 ( 14) hydrogen bonds : bond 0.03074 / 1.93 ( 206) hydrogen bonds : angle 6.40211 / 4.41 ( 525) link_ALPHA1-2 : bond 0.00333 / 0.21 ( 1) link_ALPHA1-2 : angle 1.70666 / 0.92 ( 3) link_ALPHA1-3 : bond 0.01760 / 1.10 ( 1) link_ALPHA1-3 : angle 1.39863 / 0.54 ( 3) link_ALPHA1-6 : bond 0.00739 / 0.46 ( 1) link_ALPHA1-6 : angle 1.62480 / 0.89 ( 3) link_BETA1-4 : bond 0.01013 / 0.57 ( 6) link_BETA1-4 : angle 2.59358 / 2.28 ( 18) link_NAG-ASN : bond 0.00183 / 0.13 ( 8) link_NAG-ASN : angle 1.42565 / 0.86 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3748.47 seconds wall clock time: 64 minutes 2.73 seconds (3842.73 seconds total)