Starting phenix.real_space_refine on Sat Aug 23 14:28:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vs6_43489/08_2025/8vs6_43489_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vs6_43489/08_2025/8vs6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vs6_43489/08_2025/8vs6_43489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vs6_43489/08_2025/8vs6_43489.map" model { file = "/net/cci-nas-00/data/ceres_data/8vs6_43489/08_2025/8vs6_43489_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vs6_43489/08_2025/8vs6_43489_trim.cif" } 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-2.0-5787/lib/python3.9/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, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 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, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.12, per 1000 atoms: 0.25 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: 1.10 Conformation dependent library (CDL) restraints added in 408.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 2.99 Time building geometry restraints manager: 1.54 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: 3.430 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: 0.080 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 aren 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 covalent geometry : bond 0.00435 ( 6569) covalent geometry : angle 0.73718 ( 8892) SS BOND : bond 0.00195 ( 7) SS BOND : angle 0.39306 ( 14) hydrogen bonds : bond 0.20038 ( 206) hydrogen bonds : angle 8.98055 ( 525) link_ALPHA1-2 : bond 0.00884 ( 1) link_ALPHA1-2 : angle 2.58010 ( 3) link_ALPHA1-3 : bond 0.01496 ( 1) link_ALPHA1-3 : angle 1.49691 ( 3) link_ALPHA1-6 : bond 0.00666 ( 1) link_ALPHA1-6 : angle 1.73415 ( 3) link_BETA1-4 : bond 0.01200 ( 6) link_BETA1-4 : angle 3.92514 ( 18) link_NAG-ASN : bond 0.00316 ( 8) link_NAG-ASN : angle 1.86156 ( 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 : 0.327 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: 1.1069 time to fit residues: 98.9933 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 : 0.365 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 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: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 352 GLN B 353 GLN B 422 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140758 restraints weight = 19531.282| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.58 r_work: 0.3592 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0876 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= 0.205 Angle : 0.659 10.566 8957 Z= 0.339 Chirality : 0.050 0.248 1008 Planarity : 0.005 0.057 1148 Dihedral : 9.452 80.271 1228 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.85 % Allowed : 15.44 % Favored : 81.71 % 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 aren not related in a simple way. whole: -0.59 (0.29), residues: 791 helix: -0.87 (0.50), residues: 106 sheet: 0.18 (0.30), residues: 264 loop : -0.56 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 143 TYR 0.025 0.002 TYR A 275 PHE 0.013 0.002 PHE A 217 TRP 0.013 0.002 TRP B 230 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 6569) covalent geometry : angle 0.63503 ( 8892) SS BOND : bond 0.00345 ( 7) SS BOND : angle 0.79751 ( 14) hydrogen bonds : bond 0.04364 ( 206) hydrogen bonds : angle 7.36350 ( 525) link_ALPHA1-2 : bond 0.00132 ( 1) link_ALPHA1-2 : angle 2.24534 ( 3) link_ALPHA1-3 : bond 0.01885 ( 1) link_ALPHA1-3 : angle 2.28725 ( 3) link_ALPHA1-6 : bond 0.00657 ( 1) link_ALPHA1-6 : angle 2.20527 ( 3) link_BETA1-4 : bond 0.01174 ( 6) link_BETA1-4 : angle 3.08924 ( 18) link_NAG-ASN : bond 0.00338 ( 8) link_NAG-ASN : angle 1.82035 ( 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 92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.8314 (p-90) REVERT: A 275 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: A 316 SER cc_start: 0.8006 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 369 LYS cc_start: 0.7096 (mtmm) cc_final: 0.6611 (mtpp) REVERT: B 218 MET cc_start: 0.8370 (mtp) cc_final: 0.8109 (ttm) REVERT: B 278 MET cc_start: 0.8566 (ptp) cc_final: 0.7930 (ptp) outliers start: 19 outliers final: 10 residues processed: 84 average time/residue: 0.9370 time to fit residues: 83.3547 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 : 0.220 ------------------------------------------------------------------------------- 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 236 ILE 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 416 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3917 r_free = 0.3917 target = 0.162890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141361 restraints weight = 19778.606| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.59 r_work: 0.3598 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1071 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= 0.155 Angle : 0.603 10.617 8957 Z= 0.307 Chirality : 0.047 0.220 1008 Planarity : 0.004 0.044 1148 Dihedral : 8.453 65.974 1220 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.30 % Allowed : 15.59 % Favored : 81.11 % 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 aren not related in a simple way. whole: -0.68 (0.29), residues: 791 helix: -0.71 (0.51), residues: 106 sheet: -0.03 (0.30), residues: 263 loop : -0.58 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 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 covalent geometry : bond 0.00351 ( 6569) covalent geometry : angle 0.58068 ( 8892) SS BOND : bond 0.00343 ( 7) SS BOND : angle 0.74131 ( 14) hydrogen bonds : bond 0.04006 ( 206) hydrogen bonds : angle 6.99696 ( 525) link_ALPHA1-2 : bond 0.00352 ( 1) link_ALPHA1-2 : angle 1.85962 ( 3) link_ALPHA1-3 : bond 0.02107 ( 1) link_ALPHA1-3 : angle 1.51028 ( 3) link_ALPHA1-6 : bond 0.00821 ( 1) link_ALPHA1-6 : angle 2.10984 ( 3) link_BETA1-4 : bond 0.01245 ( 6) link_BETA1-4 : angle 3.04102 ( 18) link_NAG-ASN : bond 0.00207 ( 8) link_NAG-ASN : angle 1.52368 ( 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 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7337 (m-10) REVERT: A 329 THR cc_start: 0.8341 (m) cc_final: 0.8002 (t) REVERT: A 369 LYS cc_start: 0.7009 (mtmm) cc_final: 0.6515 (mtpp) REVERT: B 80 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: B 218 MET cc_start: 0.8425 (mtp) cc_final: 0.8182 (ttm) REVERT: B 278 MET cc_start: 0.8522 (ptp) cc_final: 0.7943 (ptp) outliers start: 22 outliers final: 11 residues processed: 88 average time/residue: 0.8811 time to fit residues: 82.1667 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 : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 31 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3916 r_free = 0.3916 target = 0.162909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140942 restraints weight = 19581.365| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.62 r_work: 0.3596 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6593 Z= 0.159 Angle : 0.601 9.860 8957 Z= 0.305 Chirality : 0.047 0.235 1008 Planarity : 0.004 0.039 1148 Dihedral : 7.863 57.376 1220 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.15 % Allowed : 15.89 % Favored : 80.96 % 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 aren not related in a simple way. whole: -0.75 (0.29), residues: 791 helix: -0.63 (0.51), residues: 106 sheet: -0.17 (0.30), residues: 264 loop : -0.59 (0.29), residues: 421 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 0.011 0.002 PHE A 19 TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6569) covalent geometry : angle 0.57969 ( 8892) SS BOND : bond 0.00368 ( 7) SS BOND : angle 0.79126 ( 14) hydrogen bonds : bond 0.03491 ( 206) hydrogen bonds : angle 6.79105 ( 525) link_ALPHA1-2 : bond 0.00294 ( 1) link_ALPHA1-2 : angle 1.81591 ( 3) link_ALPHA1-3 : bond 0.01941 ( 1) link_ALPHA1-3 : angle 1.77426 ( 3) link_ALPHA1-6 : bond 0.00750 ( 1) link_ALPHA1-6 : angle 1.99403 ( 3) link_BETA1-4 : bond 0.01113 ( 6) link_BETA1-4 : angle 2.88421 ( 18) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.52391 ( 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 92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7549 (ptm160) REVERT: A 329 THR cc_start: 0.8424 (m) cc_final: 0.8059 (t) REVERT: A 353 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: A 369 LYS cc_start: 0.7020 (mtmm) cc_final: 0.6520 (mtpp) REVERT: A 390 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 80 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: B 190 GLU cc_start: 0.7003 (tp30) cc_final: 0.6558 (tp30) REVERT: B 218 MET cc_start: 0.8435 (mtp) cc_final: 0.8185 (ttm) REVERT: B 278 MET cc_start: 0.8504 (ptp) cc_final: 0.7994 (ptp) outliers start: 21 outliers final: 13 residues processed: 85 average time/residue: 0.9817 time to fit residues: 88.2925 Evaluate side-chains 87 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 236 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 ILE 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 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 416 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 31 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 320 GLN B 161 HIS B 202 GLN B 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140881 restraints weight = 19735.153| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.58 r_work: 0.3592 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1441 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= 0.178 Angle : 0.609 9.844 8957 Z= 0.308 Chirality : 0.048 0.232 1008 Planarity : 0.004 0.037 1148 Dihedral : 7.563 53.332 1219 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.60 % Allowed : 16.04 % Favored : 80.36 % 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 aren not related in a simple way. whole: -0.84 (0.29), residues: 791 helix: -0.62 (0.51), residues: 106 sheet: -0.30 (0.30), residues: 264 loop : -0.61 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.024 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 covalent geometry : bond 0.00412 ( 6569) covalent geometry : angle 0.58764 ( 8892) SS BOND : bond 0.00376 ( 7) SS BOND : angle 0.77932 ( 14) hydrogen bonds : bond 0.03545 ( 206) hydrogen bonds : angle 6.70691 ( 525) link_ALPHA1-2 : bond 0.00294 ( 1) link_ALPHA1-2 : angle 1.77362 ( 3) link_ALPHA1-3 : bond 0.02080 ( 1) link_ALPHA1-3 : angle 1.49982 ( 3) link_ALPHA1-6 : bond 0.00783 ( 1) link_ALPHA1-6 : angle 1.95588 ( 3) link_BETA1-4 : bond 0.01112 ( 6) link_BETA1-4 : angle 2.88029 ( 18) link_NAG-ASN : bond 0.00230 ( 8) link_NAG-ASN : angle 1.59519 ( 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 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7551 (ptm160) REVERT: A 329 THR cc_start: 0.8535 (m) cc_final: 0.8197 (t) REVERT: A 353 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: A 369 LYS cc_start: 0.6955 (mtmm) cc_final: 0.6511 (mtpp) REVERT: A 390 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 80 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: B 84 GLN cc_start: 0.6449 (pm20) cc_final: 0.6201 (pm20) REVERT: B 218 MET cc_start: 0.8419 (mtp) cc_final: 0.8187 (ttm) REVERT: B 278 MET cc_start: 0.8462 (ptp) cc_final: 0.7932 (ptp) outliers start: 24 outliers final: 14 residues processed: 89 average time/residue: 0.9194 time to fit residues: 86.6972 Evaluate side-chains 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS 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 A residue 353 ASP 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 362 THR 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: 1.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3899 r_free = 0.3899 target = 0.161265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139508 restraints weight = 19657.836| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.60 r_work: 0.3576 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6593 Z= 0.222 Angle : 0.647 9.751 8957 Z= 0.329 Chirality : 0.049 0.235 1008 Planarity : 0.005 0.041 1148 Dihedral : 7.337 47.154 1213 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 aren not related in a simple way. whole: -0.96 (0.29), residues: 791 helix: -0.71 (0.50), residues: 106 sheet: -0.40 (0.30), residues: 264 loop : -0.68 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.027 0.002 TYR A 275 PHE 0.015 0.002 PHE A 19 TRP 0.012 0.002 TRP B 230 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 6569) covalent geometry : angle 0.62623 ( 8892) SS BOND : bond 0.00495 ( 7) SS BOND : angle 0.80141 ( 14) hydrogen bonds : bond 0.03752 ( 206) hydrogen bonds : angle 6.77376 ( 525) link_ALPHA1-2 : bond 0.00195 ( 1) link_ALPHA1-2 : angle 1.83527 ( 3) link_ALPHA1-3 : bond 0.02211 ( 1) link_ALPHA1-3 : angle 1.35275 ( 3) link_ALPHA1-6 : bond 0.00725 ( 1) link_ALPHA1-6 : angle 1.95587 ( 3) link_BETA1-4 : bond 0.01086 ( 6) link_BETA1-4 : angle 2.87857 ( 18) link_NAG-ASN : bond 0.00297 ( 8) link_NAG-ASN : angle 1.73756 ( 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 97 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7609 (ptm160) REVERT: A 329 THR cc_start: 0.8576 (m) cc_final: 0.8236 (t) REVERT: A 353 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: A 369 LYS cc_start: 0.7092 (mtmm) cc_final: 0.6616 (mtpp) REVERT: A 390 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8477 (mp) REVERT: B 84 GLN cc_start: 0.6471 (pm20) cc_final: 0.6205 (pm20) REVERT: B 218 MET cc_start: 0.8418 (mtp) cc_final: 0.8204 (ttm) REVERT: B 278 MET cc_start: 0.8487 (ptp) cc_final: 0.7964 (ptp) outliers start: 26 outliers final: 18 residues processed: 90 average time/residue: 0.8667 time to fit residues: 82.8909 Evaluate side-chains 92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 115 ARG 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 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 358 ILE 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 357 ILE Chi-restraints excluded: chain B residue 362 THR 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: 0.9990 chunk 55 optimal weight: 1.9990 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: 0.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3906 r_free = 0.3906 target = 0.161728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140260 restraints weight = 19522.740| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.60 r_work: 0.3587 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1634 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= 0.186 Angle : 0.621 9.497 8957 Z= 0.316 Chirality : 0.048 0.230 1008 Planarity : 0.004 0.040 1148 Dihedral : 7.124 45.511 1213 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.45 % Allowed : 16.79 % 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 aren not related in a simple way. whole: -0.98 (0.29), residues: 791 helix: -0.69 (0.50), residues: 106 sheet: -0.46 (0.30), residues: 264 loop : -0.68 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.024 0.002 TYR A 275 PHE 0.013 0.002 PHE A 19 TRP 0.011 0.002 TRP B 230 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6569) covalent geometry : angle 0.60091 ( 8892) SS BOND : bond 0.00406 ( 7) SS BOND : angle 0.73369 ( 14) hydrogen bonds : bond 0.03514 ( 206) hydrogen bonds : angle 6.68621 ( 525) link_ALPHA1-2 : bond 0.00285 ( 1) link_ALPHA1-2 : angle 1.79866 ( 3) link_ALPHA1-3 : bond 0.02088 ( 1) link_ALPHA1-3 : angle 1.53533 ( 3) link_ALPHA1-6 : bond 0.00713 ( 1) link_ALPHA1-6 : angle 1.81832 ( 3) link_BETA1-4 : bond 0.01076 ( 6) link_BETA1-4 : angle 2.80788 ( 18) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 1.60799 ( 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 97 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8667 (OUTLIER) cc_final: 0.8273 (p-90) REVERT: A 115 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7598 (ptm160) REVERT: A 329 THR cc_start: 0.8523 (m) cc_final: 0.8209 (t) REVERT: A 353 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: A 369 LYS cc_start: 0.7109 (mtmm) cc_final: 0.6638 (mtpp) REVERT: A 390 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 430 ASP cc_start: 0.7758 (m-30) cc_final: 0.7519 (m-30) REVERT: B 80 GLU cc_start: 0.7834 (tt0) cc_final: 0.7629 (tt0) REVERT: B 84 GLN cc_start: 0.6494 (pm20) cc_final: 0.6053 (pm20) REVERT: B 190 GLU cc_start: 0.7006 (tp30) cc_final: 0.6707 (tp30) REVERT: B 218 MET cc_start: 0.8402 (mtp) cc_final: 0.8194 (ttm) REVERT: B 278 MET cc_start: 0.8461 (ptp) cc_final: 0.7932 (ptp) outliers start: 23 outliers final: 16 residues processed: 91 average time/residue: 0.8912 time to fit residues: 86.0720 Evaluate side-chains 91 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 137 VAL Chi-restraints excluded: chain A residue 142 CYS 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 353 ASP 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 357 ILE 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: 0.9990 chunk 69 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3920 r_free = 0.3920 target = 0.163256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141699 restraints weight = 19424.734| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.60 r_work: 0.3602 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6593 Z= 0.134 Angle : 0.576 9.224 8957 Z= 0.291 Chirality : 0.047 0.213 1008 Planarity : 0.004 0.036 1148 Dihedral : 6.599 44.367 1213 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.85 % Allowed : 17.39 % 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 aren not related in a simple way. whole: -0.92 (0.29), residues: 791 helix: -0.51 (0.51), residues: 106 sheet: -0.47 (0.30), residues: 264 loop : -0.64 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 236 TYR 0.021 0.002 TYR A 275 PHE 0.010 0.001 PHE A 88 TRP 0.009 0.001 TRP B 230 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6569) covalent geometry : angle 0.55682 ( 8892) SS BOND : bond 0.00339 ( 7) SS BOND : angle 0.71523 ( 14) hydrogen bonds : bond 0.03087 ( 206) hydrogen bonds : angle 6.47254 ( 525) link_ALPHA1-2 : bond 0.00381 ( 1) link_ALPHA1-2 : angle 1.72725 ( 3) link_ALPHA1-3 : bond 0.01802 ( 1) link_ALPHA1-3 : angle 1.73548 ( 3) link_ALPHA1-6 : bond 0.00738 ( 1) link_ALPHA1-6 : angle 1.69778 ( 3) link_BETA1-4 : bond 0.01067 ( 6) link_BETA1-4 : angle 2.69699 ( 18) link_NAG-ASN : bond 0.00171 ( 8) link_NAG-ASN : angle 1.39752 ( 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 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.8258 (p-90) REVERT: A 329 THR cc_start: 0.8581 (m) cc_final: 0.8226 (t) REVERT: A 353 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: A 369 LYS cc_start: 0.7113 (mtmm) cc_final: 0.6631 (mtpp) REVERT: B 80 GLU cc_start: 0.7875 (tt0) cc_final: 0.7666 (tt0) REVERT: B 84 GLN cc_start: 0.6415 (pm20) cc_final: 0.6032 (pm20) REVERT: B 103 TYR cc_start: 0.8257 (m-80) cc_final: 0.7969 (m-80) REVERT: B 190 GLU cc_start: 0.7110 (tp30) cc_final: 0.6889 (tp30) REVERT: B 218 MET cc_start: 0.8388 (mtp) cc_final: 0.8152 (ttm) REVERT: B 278 MET cc_start: 0.8437 (ptp) cc_final: 0.7939 (ptp) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 1.0165 time to fit residues: 99.1668 Evaluate side-chains 86 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 A residue 353 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 125 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 = 0.3923 r_free = 0.3923 target = 0.163537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142092 restraints weight = 19648.611| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.58 r_work: 0.3608 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1771 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= 0.128 Angle : 0.567 9.048 8957 Z= 0.287 Chirality : 0.046 0.199 1008 Planarity : 0.004 0.049 1148 Dihedral : 6.276 43.649 1213 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.85 % Allowed : 17.69 % 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 aren not related in a simple way. whole: -0.86 (0.29), residues: 791 helix: -0.41 (0.51), residues: 106 sheet: -0.42 (0.31), residues: 264 loop : -0.61 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 115 TYR 0.020 0.001 TYR A 275 PHE 0.009 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 covalent geometry : bond 0.00293 ( 6569) covalent geometry : angle 0.54873 ( 8892) SS BOND : bond 0.00319 ( 7) SS BOND : angle 0.70553 ( 14) hydrogen bonds : bond 0.02975 ( 206) hydrogen bonds : angle 6.34333 ( 525) link_ALPHA1-2 : bond 0.00368 ( 1) link_ALPHA1-2 : angle 1.69201 ( 3) link_ALPHA1-3 : bond 0.01708 ( 1) link_ALPHA1-3 : angle 1.52060 ( 3) link_ALPHA1-6 : bond 0.00766 ( 1) link_ALPHA1-6 : angle 1.63724 ( 3) link_BETA1-4 : bond 0.01049 ( 6) link_BETA1-4 : angle 2.63654 ( 18) link_NAG-ASN : bond 0.00165 ( 8) link_NAG-ASN : angle 1.38229 ( 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 92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.8217 (p-90) REVERT: A 115 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7607 (ptm160) REVERT: A 329 THR cc_start: 0.8577 (m) cc_final: 0.8228 (t) REVERT: A 353 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: A 369 LYS cc_start: 0.7135 (mtmm) cc_final: 0.6656 (mtpp) REVERT: B 80 GLU cc_start: 0.7838 (tt0) cc_final: 0.7604 (tt0) REVERT: B 84 GLN cc_start: 0.6417 (pm20) cc_final: 0.6040 (pm20) REVERT: B 190 GLU cc_start: 0.7100 (tp30) cc_final: 0.6890 (tp30) REVERT: B 218 MET cc_start: 0.8392 (mtp) cc_final: 0.8138 (ttm) REVERT: B 278 MET cc_start: 0.8387 (ptp) cc_final: 0.7883 (ptp) REVERT: B 393 THR cc_start: 0.8032 (m) cc_final: 0.7797 (p) outliers start: 19 outliers final: 12 residues processed: 89 average time/residue: 1.0239 time to fit residues: 96.9989 Evaluate side-chains 87 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP 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 44 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 65 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 384 ASN B 125 ASN B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.162466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140629 restraints weight = 19577.783| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.61 r_work: 0.3592 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1825 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= 0.173 Angle : 0.603 8.959 8957 Z= 0.305 Chirality : 0.047 0.198 1008 Planarity : 0.004 0.044 1148 Dihedral : 6.406 44.231 1213 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.40 % Allowed : 18.14 % 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 aren not related in a simple way. whole: -0.91 (0.29), residues: 791 helix: -0.49 (0.51), residues: 106 sheet: -0.47 (0.30), residues: 264 loop : -0.62 (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 0.012 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 covalent geometry : bond 0.00404 ( 6569) covalent geometry : angle 0.58529 ( 8892) SS BOND : bond 0.00374 ( 7) SS BOND : angle 0.72965 ( 14) hydrogen bonds : bond 0.03287 ( 206) hydrogen bonds : angle 6.43068 ( 525) link_ALPHA1-2 : bond 0.00257 ( 1) link_ALPHA1-2 : angle 1.75463 ( 3) link_ALPHA1-3 : bond 0.01921 ( 1) link_ALPHA1-3 : angle 1.25826 ( 3) link_ALPHA1-6 : bond 0.00743 ( 1) link_ALPHA1-6 : angle 1.69832 ( 3) link_BETA1-4 : bond 0.01013 ( 6) link_BETA1-4 : angle 2.64066 ( 18) link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 1.52094 ( 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 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.8167 (p-90) REVERT: A 115 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7642 (ptm160) REVERT: A 329 THR cc_start: 0.8687 (m) cc_final: 0.8353 (t) REVERT: A 353 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: A 369 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6692 (mtpp) REVERT: B 80 GLU cc_start: 0.7864 (tt0) cc_final: 0.7605 (tt0) REVERT: B 84 GLN cc_start: 0.6431 (pm20) cc_final: 0.6049 (pm20) REVERT: B 218 MET cc_start: 0.8399 (mtp) cc_final: 0.8174 (ttm) REVERT: B 278 MET cc_start: 0.8416 (ptp) cc_final: 0.7912 (ptp) REVERT: B 393 THR cc_start: 0.8059 (m) cc_final: 0.7831 (p) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.9736 time to fit residues: 88.9174 Evaluate side-chains 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP 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 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: 0.6980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 125 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 = 0.3917 r_free = 0.3917 target = 0.162921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141178 restraints weight = 19526.007| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.61 r_work: 0.3598 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6593 Z= 0.159 Angle : 0.590 8.828 8957 Z= 0.299 Chirality : 0.047 0.194 1008 Planarity : 0.004 0.045 1148 Dihedral : 6.341 44.015 1213 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.85 % Allowed : 17.84 % Favored : 79.31 % 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 aren not related in a simple way. whole: -0.88 (0.29), residues: 791 helix: -0.43 (0.52), residues: 106 sheet: -0.47 (0.30), residues: 264 loop : -0.60 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.021 0.002 TYR A 275 PHE 0.011 0.002 PHE A 19 TRP 0.009 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6569) covalent geometry : angle 0.57222 ( 8892) SS BOND : bond 0.00374 ( 7) SS BOND : angle 0.70468 ( 14) hydrogen bonds : bond 0.03180 ( 206) hydrogen bonds : angle 6.39369 ( 525) link_ALPHA1-2 : bond 0.00297 ( 1) link_ALPHA1-2 : angle 1.74608 ( 3) link_ALPHA1-3 : bond 0.01831 ( 1) link_ALPHA1-3 : angle 1.36688 ( 3) link_ALPHA1-6 : bond 0.00704 ( 1) link_ALPHA1-6 : angle 1.63765 ( 3) link_BETA1-4 : bond 0.01005 ( 6) link_BETA1-4 : angle 2.60108 ( 18) link_NAG-ASN : bond 0.00207 ( 8) link_NAG-ASN : angle 1.44407 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3952.48 seconds wall clock time: 67 minutes 35.39 seconds (4055.39 seconds total)