Starting phenix.real_space_refine on Sat Jan 18 18:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vs6_43489/01_2025/8vs6_43489_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vs6_43489/01_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_43489/01_2025/8vs6_43489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vs6_43489/01_2025/8vs6_43489.map" model { file = "/net/cci-nas-00/data/ceres_data/8vs6_43489/01_2025/8vs6_43489_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vs6_43489/01_2025/8vs6_43489_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.65, per 1000 atoms: 0.53 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: 3.56 Conformation dependent library (CDL) restraints added in 976.8 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: 1.18 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: 4.26 Time building geometry restraints manager: 4.06 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: 3.200 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: 0.210 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 29.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- 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 6569 Z= 0.283 Angle : 0.737 8.494 8892 Z= 0.377 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (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 TRP 0.009 0.002 TRP B 230 HIS 0.003 0.001 HIS B 98 PHE 0.009 0.001 PHE A 88 TYR 0.025 0.002 TYR A 419 ARG 0.004 0.001 ARG B 378 *********************** 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 : 0.972 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: 2.5462 time to fit residues: 228.5540 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 : 1.044 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3904 r_free = 0.3904 target = 0.161650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140238 restraints weight = 19385.617| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.57 r_work: 0.3588 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6569 Z= 0.349 Angle : 0.652 5.182 8892 Z= 0.345 Chirality : 0.050 0.248 1008 Planarity : 0.005 0.055 1148 Dihedral : 9.577 81.142 1228 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.70 % Allowed : 15.89 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 791 helix: -0.93 (0.49), residues: 106 sheet: 0.17 (0.30), residues: 264 loop : -0.57 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 230 HIS 0.004 0.001 HIS B 227 PHE 0.015 0.002 PHE A 217 TYR 0.026 0.002 TYR A 275 ARG 0.004 0.001 ARG A 143 *********************** 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: 18 poor density : 74 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8619 (OUTLIER) cc_final: 0.8333 (p-90) REVERT: A 275 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: A 316 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7799 (p) REVERT: A 369 LYS cc_start: 0.7125 (mtmm) cc_final: 0.6636 (mtpp) REVERT: B 80 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: B 218 MET cc_start: 0.8350 (mtp) cc_final: 0.8096 (ttm) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 2.2633 time to fit residues: 203.9493 Evaluate side-chains 84 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.161731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140059 restraints weight = 19723.105| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.60 r_work: 0.3585 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6569 Z= 0.291 Angle : 0.614 5.322 8892 Z= 0.320 Chirality : 0.048 0.220 1008 Planarity : 0.005 0.043 1148 Dihedral : 8.589 64.582 1220 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.05 % Allowed : 15.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 791 helix: -0.88 (0.49), residues: 106 sheet: -0.08 (0.30), residues: 264 loop : -0.62 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 230 HIS 0.003 0.001 HIS B 180 PHE 0.014 0.002 PHE A 19 TYR 0.024 0.002 TYR A 275 ARG 0.004 0.001 ARG A 168 *********************** 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 103 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: A 329 THR cc_start: 0.8371 (m) cc_final: 0.8013 (t) REVERT: A 353 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: A 369 LYS cc_start: 0.7013 (mtmm) cc_final: 0.6503 (mtpp) REVERT: A 390 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 80 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: B 218 MET cc_start: 0.8394 (mtp) cc_final: 0.8167 (ttm) outliers start: 27 outliers final: 14 residues processed: 94 average time/residue: 2.2616 time to fit residues: 225.6013 Evaluate side-chains 90 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 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 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.161443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139805 restraints weight = 19595.543| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.59 r_work: 0.3582 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6569 Z= 0.307 Angle : 0.617 5.516 8892 Z= 0.321 Chirality : 0.048 0.239 1008 Planarity : 0.004 0.040 1148 Dihedral : 8.217 56.473 1220 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.60 % Allowed : 17.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 791 helix: -0.86 (0.50), residues: 106 sheet: -0.18 (0.30), residues: 264 loop : -0.67 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 PHE 0.013 0.002 PHE A 19 TYR 0.026 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 *********************** 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 98 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7561 (ptm160) REVERT: A 329 THR cc_start: 0.8445 (m) cc_final: 0.8064 (t) REVERT: A 353 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A 369 LYS cc_start: 0.7058 (mtmm) cc_final: 0.6579 (mtpp) REVERT: B 80 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: B 202 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: B 218 MET cc_start: 0.8416 (mtp) cc_final: 0.8199 (ttm) outliers start: 24 outliers final: 16 residues processed: 91 average time/residue: 2.3547 time to fit residues: 226.9764 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 : 1.008 ------------------------------------------------------------------------------- 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 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 80 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN 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 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 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 73 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 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 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140440 restraints weight = 19577.453| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.60 r_work: 0.3587 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6569 Z= 0.250 Angle : 0.587 5.561 8892 Z= 0.304 Chirality : 0.047 0.233 1008 Planarity : 0.004 0.038 1148 Dihedral : 7.716 48.522 1220 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.75 % Allowed : 16.64 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.29), residues: 791 helix: -0.71 (0.50), residues: 106 sheet: -0.31 (0.30), residues: 264 loop : -0.66 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 118 PHE 0.011 0.002 PHE A 19 TYR 0.024 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 *********************** 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 100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7577 (ptm160) REVERT: A 329 THR cc_start: 0.8550 (m) cc_final: 0.8206 (t) REVERT: A 369 LYS cc_start: 0.7010 (mtmm) cc_final: 0.6560 (mtpp) REVERT: A 390 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 430 ASP cc_start: 0.7769 (m-30) cc_final: 0.7531 (m-30) REVERT: B 84 GLN cc_start: 0.6446 (pm20) cc_final: 0.6185 (pm20) REVERT: B 202 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6232 (tm-30) REVERT: B 218 MET cc_start: 0.8420 (mtp) cc_final: 0.8190 (ttm) REVERT: B 278 MET cc_start: 0.8507 (ptp) cc_final: 0.7935 (ptp) outliers start: 25 outliers final: 18 residues processed: 94 average time/residue: 2.5098 time to fit residues: 249.7905 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 : 0.971 ------------------------------------------------------------------------------- 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 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 202 GLN 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 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 152 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 = 0.3892 r_free = 0.3892 target = 0.160662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139058 restraints weight = 19876.243| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.60 r_work: 0.3575 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6569 Z= 0.353 Angle : 0.635 5.981 8892 Z= 0.329 Chirality : 0.049 0.235 1008 Planarity : 0.005 0.043 1148 Dihedral : 7.845 55.333 1220 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.90 % Allowed : 17.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.28), residues: 791 helix: -0.86 (0.49), residues: 106 sheet: -0.39 (0.30), residues: 264 loop : -0.69 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 230 HIS 0.004 0.001 HIS B 307 PHE 0.014 0.002 PHE A 217 TYR 0.026 0.002 TYR A 275 ARG 0.004 0.000 ARG B 236 *********************** 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 101 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7529 (ptm160) REVERT: A 329 THR cc_start: 0.8559 (m) cc_final: 0.8221 (t) REVERT: A 353 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: A 369 LYS cc_start: 0.7169 (mtmm) cc_final: 0.6689 (mtpp) REVERT: A 390 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8489 (mp) REVERT: A 430 ASP cc_start: 0.7788 (m-30) cc_final: 0.7552 (m-30) REVERT: B 84 GLN cc_start: 0.6424 (pm20) cc_final: 0.6025 (pm20) REVERT: B 202 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.6180 (tm-30) REVERT: B 218 MET cc_start: 0.8393 (mtp) cc_final: 0.8189 (ttm) REVERT: B 278 MET cc_start: 0.8543 (ptp) cc_final: 0.7979 (ptp) outliers start: 26 outliers final: 17 residues processed: 95 average time/residue: 2.2053 time to fit residues: 222.6676 Evaluate side-chains 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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 202 GLN 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 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140390 restraints weight = 19646.999| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.61 r_work: 0.3589 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6569 Z= 0.241 Angle : 0.582 5.655 8892 Z= 0.301 Chirality : 0.047 0.228 1008 Planarity : 0.004 0.039 1148 Dihedral : 7.411 59.337 1218 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.45 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.28), residues: 791 helix: -0.71 (0.50), residues: 106 sheet: -0.44 (0.30), residues: 264 loop : -0.67 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 118 PHE 0.011 0.002 PHE A 19 TYR 0.023 0.002 TYR A 275 ARG 0.002 0.000 ARG B 236 *********************** 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 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 THR cc_start: 0.8515 (m) cc_final: 0.8203 (t) REVERT: A 353 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: A 369 LYS cc_start: 0.7111 (mtmm) cc_final: 0.6628 (mtpp) REVERT: A 390 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 80 GLU cc_start: 0.7847 (tt0) cc_final: 0.7647 (tt0) REVERT: B 84 GLN cc_start: 0.6425 (pm20) cc_final: 0.6019 (pm20) REVERT: B 190 GLU cc_start: 0.6995 (tp30) cc_final: 0.6703 (tp30) REVERT: B 202 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: B 218 MET cc_start: 0.8393 (mtp) cc_final: 0.8188 (ttm) REVERT: B 278 MET cc_start: 0.8470 (ptp) cc_final: 0.7890 (ptp) outliers start: 23 outliers final: 14 residues processed: 90 average time/residue: 2.3863 time to fit residues: 227.5198 Evaluate side-chains 90 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 142 CYS 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 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 202 GLN 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 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.162478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140944 restraints weight = 19642.835| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.61 r_work: 0.3597 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6569 Z= 0.230 Angle : 0.571 5.618 8892 Z= 0.295 Chirality : 0.047 0.217 1008 Planarity : 0.004 0.044 1148 Dihedral : 6.760 43.590 1213 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.45 % Allowed : 18.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 791 helix: -0.62 (0.50), residues: 106 sheet: -0.42 (0.30), residues: 264 loop : -0.66 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 118 PHE 0.010 0.002 PHE A 19 TYR 0.021 0.002 TYR A 275 ARG 0.004 0.000 ARG A 143 *********************** 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 101 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7643 (ptm160) REVERT: A 329 THR cc_start: 0.8609 (m) cc_final: 0.8242 (t) REVERT: A 353 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6763 (m-30) REVERT: A 369 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6657 (mtpp) REVERT: A 390 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 84 GLN cc_start: 0.6424 (pm20) cc_final: 0.6024 (pm20) REVERT: B 202 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.6131 (tm-30) REVERT: B 218 MET cc_start: 0.8389 (mtp) cc_final: 0.8177 (ttm) REVERT: B 278 MET cc_start: 0.8483 (ptp) cc_final: 0.7975 (ptp) outliers start: 23 outliers final: 15 residues processed: 95 average time/residue: 2.5241 time to fit residues: 255.7372 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 : 0.930 ------------------------------------------------------------------------------- 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 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 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 202 GLN 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 31 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 57 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.162715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141098 restraints weight = 19518.452| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.60 r_work: 0.3600 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6569 Z= 0.225 Angle : 0.567 5.634 8892 Z= 0.293 Chirality : 0.047 0.208 1008 Planarity : 0.004 0.043 1148 Dihedral : 6.537 43.648 1213 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.30 % Allowed : 18.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.29), residues: 791 helix: -0.54 (0.51), residues: 106 sheet: -0.41 (0.30), residues: 264 loop : -0.62 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 230 HIS 0.003 0.001 HIS B 98 PHE 0.010 0.002 PHE A 19 TYR 0.021 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 *********************** 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 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7652 (ptm160) REVERT: A 329 THR cc_start: 0.8615 (m) cc_final: 0.8257 (t) REVERT: A 353 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: A 369 LYS cc_start: 0.7196 (mtmm) cc_final: 0.6705 (mtpp) REVERT: B 84 GLN cc_start: 0.6430 (pm20) cc_final: 0.6033 (pm20) REVERT: B 202 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.6176 (tm-30) REVERT: B 218 MET cc_start: 0.8385 (mtp) cc_final: 0.8150 (ttm) REVERT: B 278 MET cc_start: 0.8464 (ptp) cc_final: 0.7955 (ptp) outliers start: 22 outliers final: 14 residues processed: 91 average time/residue: 2.2680 time to fit residues: 219.1961 Evaluate side-chains 86 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 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 202 GLN 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 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.163370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141730 restraints weight = 19364.038| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.60 r_work: 0.3604 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6569 Z= 0.207 Angle : 0.557 5.549 8892 Z= 0.287 Chirality : 0.047 0.194 1008 Planarity : 0.004 0.041 1148 Dihedral : 6.288 43.514 1213 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.70 % Allowed : 18.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.29), residues: 791 helix: -0.45 (0.51), residues: 106 sheet: -0.44 (0.30), residues: 264 loop : -0.58 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.003 0.001 HIS B 98 PHE 0.009 0.001 PHE A 88 TYR 0.020 0.001 TYR A 275 ARG 0.003 0.000 ARG A 143 ********************** 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: 18 poor density : 70 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7653 (ptm160) REVERT: A 329 THR cc_start: 0.8694 (m) cc_final: 0.8357 (t) REVERT: A 353 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: A 369 LYS cc_start: 0.7202 (mtmm) cc_final: 0.6711 (mtpp) REVERT: B 84 GLN cc_start: 0.6422 (pm20) cc_final: 0.6072 (pm20) REVERT: B 202 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: B 218 MET cc_start: 0.8375 (mtp) cc_final: 0.8131 (ttm) REVERT: B 278 MET cc_start: 0.8443 (ptp) cc_final: 0.7867 (ptp) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 2.3466 time to fit residues: 213.8299 Evaluate side-chains 85 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 164 ARG Chi-restraints excluded: chain B residue 202 GLN 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 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140683 restraints weight = 19563.034| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.61 r_work: 0.3593 rms_B_bonded: 1.76 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: 0.7822 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6569 Z= 0.274 Angle : 0.590 5.772 8892 Z= 0.303 Chirality : 0.048 0.195 1008 Planarity : 0.004 0.045 1148 Dihedral : 6.415 44.450 1213 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.85 % Allowed : 18.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.29), residues: 791 helix: -0.52 (0.51), residues: 106 sheet: -0.48 (0.30), residues: 264 loop : -0.62 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 PHE 0.012 0.002 PHE A 19 TYR 0.021 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8617.13 seconds wall clock time: 154 minutes 25.86 seconds (9265.86 seconds total)