Starting phenix.real_space_refine on Wed Feb 4 20:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6n_62130/02_2026/9k6n_62130_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6n_62130/02_2026/9k6n_62130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k6n_62130/02_2026/9k6n_62130_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6n_62130/02_2026/9k6n_62130_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6n_62130/02_2026/9k6n_62130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6n_62130/02_2026/9k6n_62130.map" } resolution = 3.14 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= 0.001 sd= 0.057 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 4048 2.51 5 N 1080 2.21 5 O 1212 1.98 5 H 6156 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12536 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3081 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain: "B" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3159 Classifications: {'peptide': 209} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "G" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3081 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain: "H" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3159 Classifications: {'peptide': 209} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.21 Number of scatterers: 12536 At special positions: 0 Unit cell: (113.715, 100.035, 58.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1212 8.00 N 1080 7.00 C 4048 6.00 H 6156 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS H 318 " distance=2.05 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS H 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS G 317 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 357 " distance=2.04 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 357 " 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 NAG-ASN " NAG A1000 " - " ASN A 220 " " NAG B1000 " - " ASN B 220 " " NAG G1000 " - " ASN G 220 " " NAG H1000 " - " ASN H 220 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 470.0 milliseconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 10 sheets defined 8.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.846A pdb=" N ARG A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.561A pdb=" N HIS A 358 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'G' and resid 324 through 328 Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.867A pdb=" N ARG G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY G 352 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 4.474A pdb=" N CYS G 357 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS G 358 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 328 removed outlier: 3.586A pdb=" N ALA H 328 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 185 removed outlier: 6.057A pdb=" N LEU A 333 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LYS A 214 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY A 335 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TRP A 212 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 208 " --> pdb=" O TRP A 339 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 281 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR A 292 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 283 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 228 removed outlier: 3.589A pdb=" N GLN A 309 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 228 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU A 308 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 197 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU A 370 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 185 removed outlier: 3.616A pdb=" N ARG B 332 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 334 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 273 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 282 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 291 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 285 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 258 removed outlier: 3.637A pdb=" N ILE B 245 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 236 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B 226 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 238 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 308 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 196 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 193 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU B 370 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 288 through 293 removed outlier: 5.103A pdb=" N LEU G 289 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL G 285 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA G 291 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 208 " --> pdb=" O TRP G 339 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRP G 212 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLY G 335 " --> pdb=" O TRP G 212 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LYS G 214 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU G 333 " --> pdb=" O LYS G 214 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 378 " --> pdb=" O LEU G 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 225 through 228 removed outlier: 3.598A pdb=" N GLY G 228 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU G 308 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER G 195 " --> pdb=" O GLN G 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AA9, first strand: chain 'H' and resid 288 through 293 removed outlier: 5.238A pdb=" N LEU H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL H 285 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 291 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER H 282 " --> pdb=" O THR H 273 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA H 209 " --> pdb=" O GLY H 272 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP H 212 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY H 335 " --> pdb=" O TRP H 212 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS H 214 " --> pdb=" O LEU H 333 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU H 333 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 257 through 259 removed outlier: 3.963A pdb=" N PHE H 225 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU H 240 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE H 223 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU H 308 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 196 " --> pdb=" O LEU H 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE H 193 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU H 370 " --> pdb=" O HIS H 197 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 408 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: 2.62 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6156 1.04 - 1.23: 260 1.23 - 1.43: 2522 1.43 - 1.63: 3688 1.63 - 1.82: 56 Bond restraints: 12682 Sorted by residual: bond pdb=" N SER H 173 " pdb=" H1 SER H 173 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N SER B 173 " pdb=" H1 SER B 173 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG A1000 " pdb=" O5 NAG A1000 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" C1 NAG G1000 " pdb=" O5 NAG G1000 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 12677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 22830 7.12 - 14.23: 0 14.23 - 21.35: 0 21.35 - 28.46: 0 28.46 - 35.58: 6 Bond angle restraints: 22836 Sorted by residual: angle pdb=" C GLU A 180 " pdb=" CA GLU A 180 " pdb=" HA GLU A 180 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C CYS G 179 " pdb=" CA CYS G 179 " pdb=" HA CYS G 179 " ideal model delta sigma weight residual 109.00 74.06 34.94 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" HA GLU A 180 " ideal model delta sigma weight residual 110.00 75.07 34.93 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N CYS G 179 " pdb=" CA CYS G 179 " pdb=" HA CYS G 179 " ideal model delta sigma weight residual 110.00 75.97 34.03 3.00e+00 1.11e-01 1.29e+02 angle pdb=" CB CYS G 179 " pdb=" CA CYS G 179 " pdb=" HA CYS G 179 " ideal model delta sigma weight residual 109.00 75.92 33.08 3.00e+00 1.11e-01 1.22e+02 ... (remaining 22831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 5570 23.48 - 46.96: 349 46.96 - 70.45: 78 70.45 - 93.93: 20 93.93 - 117.41: 4 Dihedral angle restraints: 6021 sinusoidal: 3275 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS H 317 " pdb=" CB CYS H 317 " ideal model delta sinusoidal sigma weight residual -86.00 -175.91 89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS H 318 " pdb=" CB CYS H 318 " ideal model delta sinusoidal sigma weight residual 93.00 18.49 74.51 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CB CYS B 317 " pdb=" SG CYS B 317 " pdb=" SG CYS G 318 " pdb=" CB CYS G 318 " ideal model delta sinusoidal sigma weight residual -86.00 -149.67 63.67 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 6018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 862 0.081 - 0.161: 124 0.161 - 0.242: 0 0.242 - 0.323: 0 0.323 - 0.404: 2 Chirality restraints: 988 Sorted by residual: chirality pdb=" CA CYS G 179 " pdb=" N CYS G 179 " pdb=" C CYS G 179 " pdb=" CB CYS G 179 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA GLU A 180 " pdb=" N GLU A 180 " pdb=" C GLU A 180 " pdb=" CB GLU A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA ILE H 236 " pdb=" N ILE H 236 " pdb=" C ILE H 236 " pdb=" CB ILE H 236 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 985 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 232 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 233 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 232 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO H 233 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO H 233 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 233 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 175 " 0.015 5.00e-02 4.00e+02 2.31e-02 8.57e-01 pdb=" N PRO B 176 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.013 5.00e-02 4.00e+02 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 477 2.17 - 2.78: 23978 2.78 - 3.38: 32517 3.38 - 3.99: 43341 3.99 - 4.60: 67520 Nonbonded interactions: 167833 Sorted by model distance: nonbonded pdb=" H GLU A 180 " pdb=" HA GLU A 180 " model vdw 1.559 1.816 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.610 2.450 nonbonded pdb=" O LEU A 224 " pdb=" H GLY A 311 " model vdw 1.612 2.450 nonbonded pdb=" O LEU G 224 " pdb=" H GLY G 311 " model vdw 1.616 2.450 nonbonded pdb=" HA GLU A 180 " pdb=" HB2 GLU A 180 " model vdw 1.642 1.952 ... (remaining 167828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 178 through 1000) selection = chain 'G' selection = (chain 'H' and resid 178 through 1000) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.060 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.490 Find NCS groups from input model: 0.190 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.003 0.051 6539 Z= 0.120 Angle : 0.481 5.151 8884 Z= 0.255 Chirality : 0.049 0.404 988 Planarity : 0.003 0.033 1126 Dihedral : 15.885 117.410 2358 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.30), residues: 818 helix: 0.12 (1.07), residues: 28 sheet: -1.06 (0.34), residues: 252 loop : -1.07 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.007 0.001 TYR A 239 PHE 0.009 0.001 PHE B 207 TRP 0.006 0.001 TRP G 267 HIS 0.008 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6526) covalent geometry : angle 0.47194 ( 8854) SS BOND : bond 0.00620 ( 9) SS BOND : angle 1.68743 ( 18) hydrogen bonds : bond 0.27823 ( 178) hydrogen bonds : angle 10.73417 ( 408) link_NAG-ASN : bond 0.00430 ( 4) link_NAG-ASN : angle 1.64512 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2822 time to fit residues: 46.2041 Evaluate side-chains 119 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120015 restraints weight = 23707.935| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 4.56 r_work: 0.3425 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6539 Z= 0.098 Angle : 0.514 4.771 8884 Z= 0.271 Chirality : 0.050 0.388 988 Planarity : 0.003 0.035 1126 Dihedral : 11.270 107.282 958 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.30), residues: 818 helix: -0.38 (0.86), residues: 34 sheet: -0.89 (0.33), residues: 266 loop : -1.09 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 203 TYR 0.013 0.001 TYR A 239 PHE 0.010 0.001 PHE H 225 TRP 0.006 0.001 TRP A 212 HIS 0.007 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6526) covalent geometry : angle 0.50536 ( 8854) SS BOND : bond 0.00327 ( 9) SS BOND : angle 1.39602 ( 18) hydrogen bonds : bond 0.04048 ( 178) hydrogen bonds : angle 7.55025 ( 408) link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 2.10048 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8125 (tt0) cc_final: 0.7884 (tt0) REVERT: G 275 ASN cc_start: 0.7491 (t0) cc_final: 0.7257 (t0) REVERT: G 340 ASP cc_start: 0.8201 (p0) cc_final: 0.7927 (p0) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.2465 time to fit residues: 37.6372 Evaluate side-chains 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.159369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118062 restraints weight = 24050.773| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.64 r_work: 0.3369 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6539 Z= 0.118 Angle : 0.503 4.537 8884 Z= 0.265 Chirality : 0.049 0.383 988 Planarity : 0.003 0.046 1126 Dihedral : 11.026 107.270 958 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.44 % Allowed : 6.95 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.30), residues: 818 helix: 0.33 (0.93), residues: 32 sheet: -1.08 (0.32), residues: 276 loop : -1.11 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 203 TYR 0.015 0.001 TYR A 239 PHE 0.014 0.001 PHE G 225 TRP 0.006 0.001 TRP G 212 HIS 0.007 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6526) covalent geometry : angle 0.49414 ( 8854) SS BOND : bond 0.00287 ( 9) SS BOND : angle 1.31769 ( 18) hydrogen bonds : bond 0.03673 ( 178) hydrogen bonds : angle 6.74339 ( 408) link_NAG-ASN : bond 0.00351 ( 4) link_NAG-ASN : angle 2.14555 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7797 (tpp) cc_final: 0.7441 (tpp) REVERT: G 275 ASN cc_start: 0.7568 (t0) cc_final: 0.7344 (t0) REVERT: G 340 ASP cc_start: 0.8204 (p0) cc_final: 0.7875 (p0) REVERT: H 278 GLU cc_start: 0.8758 (tp30) cc_final: 0.8510 (tp30) outliers start: 3 outliers final: 2 residues processed: 123 average time/residue: 0.2876 time to fit residues: 42.3282 Evaluate side-chains 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN B 315 ASN H 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115249 restraints weight = 24136.184| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.57 r_work: 0.3355 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6539 Z= 0.191 Angle : 0.549 4.849 8884 Z= 0.293 Chirality : 0.050 0.384 988 Planarity : 0.004 0.042 1126 Dihedral : 10.841 104.626 958 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.89 % Allowed : 8.28 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.29), residues: 818 helix: 0.59 (0.97), residues: 32 sheet: -1.04 (0.32), residues: 266 loop : -1.32 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 203 TYR 0.017 0.002 TYR A 239 PHE 0.020 0.002 PHE G 225 TRP 0.007 0.001 TRP G 212 HIS 0.006 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6526) covalent geometry : angle 0.54114 ( 8854) SS BOND : bond 0.00361 ( 9) SS BOND : angle 1.38624 ( 18) hydrogen bonds : bond 0.03760 ( 178) hydrogen bonds : angle 6.54581 ( 408) link_NAG-ASN : bond 0.00292 ( 4) link_NAG-ASN : angle 2.09204 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6594 (pm20) REVERT: G 275 ASN cc_start: 0.7669 (t0) cc_final: 0.7436 (t0) REVERT: G 340 ASP cc_start: 0.8234 (p0) cc_final: 0.7881 (p0) REVERT: H 340 ASP cc_start: 0.7674 (p0) cc_final: 0.7410 (p0) outliers start: 6 outliers final: 5 residues processed: 127 average time/residue: 0.2791 time to fit residues: 42.1007 Evaluate side-chains 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118528 restraints weight = 24009.732| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.56 r_work: 0.3397 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6539 Z= 0.100 Angle : 0.502 5.304 8884 Z= 0.262 Chirality : 0.049 0.382 988 Planarity : 0.003 0.043 1126 Dihedral : 10.533 103.294 958 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.59 % Allowed : 8.88 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.29), residues: 818 helix: 0.94 (0.96), residues: 32 sheet: -1.22 (0.31), residues: 280 loop : -1.21 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 332 TYR 0.013 0.001 TYR A 239 PHE 0.012 0.001 PHE G 225 TRP 0.007 0.001 TRP A 212 HIS 0.006 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6526) covalent geometry : angle 0.49226 ( 8854) SS BOND : bond 0.00363 ( 9) SS BOND : angle 1.42410 ( 18) hydrogen bonds : bond 0.03055 ( 178) hydrogen bonds : angle 6.28198 ( 408) link_NAG-ASN : bond 0.00404 ( 4) link_NAG-ASN : angle 2.23725 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 261 MET cc_start: 0.7558 (pmm) cc_final: 0.7331 (pmm) REVERT: G 275 ASN cc_start: 0.7573 (t0) cc_final: 0.7309 (t0) REVERT: G 340 ASP cc_start: 0.8212 (p0) cc_final: 0.7829 (p0) REVERT: H 278 GLU cc_start: 0.8756 (tp30) cc_final: 0.8509 (tp30) REVERT: H 340 ASP cc_start: 0.7816 (p0) cc_final: 0.7542 (p0) outliers start: 4 outliers final: 3 residues processed: 128 average time/residue: 0.2496 time to fit residues: 38.5618 Evaluate side-chains 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.163808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122483 restraints weight = 23673.061| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 4.67 r_work: 0.3427 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6539 Z= 0.121 Angle : 0.514 5.805 8884 Z= 0.266 Chirality : 0.049 0.382 988 Planarity : 0.004 0.048 1126 Dihedral : 10.190 100.065 958 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.04 % Allowed : 9.62 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.29), residues: 818 helix: 1.08 (0.94), residues: 32 sheet: -1.28 (0.31), residues: 280 loop : -1.19 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 332 TYR 0.015 0.001 TYR H 239 PHE 0.014 0.001 PHE G 225 TRP 0.007 0.001 TRP A 212 HIS 0.006 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6526) covalent geometry : angle 0.50467 ( 8854) SS BOND : bond 0.00336 ( 9) SS BOND : angle 1.34659 ( 18) hydrogen bonds : bond 0.03029 ( 178) hydrogen bonds : angle 6.11664 ( 408) link_NAG-ASN : bond 0.00361 ( 4) link_NAG-ASN : angle 2.17459 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7534 (pmm) cc_final: 0.7123 (pmm) REVERT: B 333 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.7030 (mp) REVERT: G 261 MET cc_start: 0.7540 (pmm) cc_final: 0.7272 (pmm) REVERT: G 275 ASN cc_start: 0.7456 (t0) cc_final: 0.7221 (t0) REVERT: G 340 ASP cc_start: 0.8128 (p0) cc_final: 0.7736 (p0) REVERT: H 278 GLU cc_start: 0.8748 (tp30) cc_final: 0.8491 (tp30) REVERT: H 340 ASP cc_start: 0.7702 (p0) cc_final: 0.7405 (p0) outliers start: 7 outliers final: 5 residues processed: 125 average time/residue: 0.2969 time to fit residues: 44.1780 Evaluate side-chains 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118036 restraints weight = 23958.126| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 4.55 r_work: 0.3374 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6539 Z= 0.115 Angle : 0.509 6.208 8884 Z= 0.263 Chirality : 0.049 0.383 988 Planarity : 0.004 0.050 1126 Dihedral : 9.983 99.436 958 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.18 % Allowed : 9.62 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.29), residues: 818 helix: 0.96 (0.91), residues: 34 sheet: -1.30 (0.31), residues: 280 loop : -1.16 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 332 TYR 0.014 0.001 TYR A 239 PHE 0.013 0.001 PHE G 225 TRP 0.007 0.001 TRP A 212 HIS 0.005 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6526) covalent geometry : angle 0.49882 ( 8854) SS BOND : bond 0.00347 ( 9) SS BOND : angle 1.32857 ( 18) hydrogen bonds : bond 0.02955 ( 178) hydrogen bonds : angle 6.03035 ( 408) link_NAG-ASN : bond 0.00376 ( 4) link_NAG-ASN : angle 2.34678 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7524 (pmm) cc_final: 0.7020 (pmm) REVERT: B 333 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7200 (mp) REVERT: G 261 MET cc_start: 0.7580 (pmm) cc_final: 0.7316 (pmm) REVERT: G 275 ASN cc_start: 0.7525 (t0) cc_final: 0.7271 (t0) REVERT: G 340 ASP cc_start: 0.8170 (p0) cc_final: 0.7791 (p0) REVERT: H 278 GLU cc_start: 0.8727 (tp30) cc_final: 0.8450 (tp30) REVERT: H 340 ASP cc_start: 0.7787 (p0) cc_final: 0.7484 (p0) outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 0.2566 time to fit residues: 38.3138 Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118232 restraints weight = 23835.505| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.60 r_work: 0.3370 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6539 Z= 0.106 Angle : 0.506 6.575 8884 Z= 0.260 Chirality : 0.049 0.385 988 Planarity : 0.004 0.054 1126 Dihedral : 9.642 96.617 958 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.18 % Allowed : 10.06 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.29), residues: 818 helix: 1.27 (0.91), residues: 34 sheet: -1.30 (0.31), residues: 280 loop : -1.12 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 332 TYR 0.014 0.001 TYR H 239 PHE 0.012 0.001 PHE G 225 TRP 0.007 0.001 TRP A 212 HIS 0.005 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6526) covalent geometry : angle 0.49644 ( 8854) SS BOND : bond 0.00338 ( 9) SS BOND : angle 1.28185 ( 18) hydrogen bonds : bond 0.02824 ( 178) hydrogen bonds : angle 5.93966 ( 408) link_NAG-ASN : bond 0.00372 ( 4) link_NAG-ASN : angle 2.30701 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7512 (pmm) cc_final: 0.6976 (pmm) REVERT: B 288 GLU cc_start: 0.7826 (mm-30) cc_final: 0.6665 (pm20) REVERT: G 261 MET cc_start: 0.7571 (pmm) cc_final: 0.7294 (pmm) REVERT: G 275 ASN cc_start: 0.7516 (t0) cc_final: 0.7258 (t0) REVERT: G 340 ASP cc_start: 0.8133 (p0) cc_final: 0.7747 (p0) REVERT: H 217 ASP cc_start: 0.7920 (t0) cc_final: 0.6903 (m-30) REVERT: H 278 GLU cc_start: 0.8702 (tp30) cc_final: 0.8414 (tp30) REVERT: H 340 ASP cc_start: 0.7778 (p0) cc_final: 0.7473 (p0) outliers start: 8 outliers final: 5 residues processed: 123 average time/residue: 0.2703 time to fit residues: 39.8498 Evaluate side-chains 121 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115848 restraints weight = 24489.562| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.60 r_work: 0.3360 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6539 Z= 0.161 Angle : 0.551 6.828 8884 Z= 0.287 Chirality : 0.050 0.387 988 Planarity : 0.004 0.058 1126 Dihedral : 9.561 96.779 958 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.33 % Allowed : 10.06 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.29), residues: 818 helix: 1.30 (0.92), residues: 34 sheet: -1.14 (0.32), residues: 266 loop : -1.28 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 332 TYR 0.015 0.002 TYR A 239 PHE 0.018 0.002 PHE G 225 TRP 0.007 0.001 TRP G 212 HIS 0.005 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6526) covalent geometry : angle 0.54073 ( 8854) SS BOND : bond 0.00510 ( 9) SS BOND : angle 1.43451 ( 18) hydrogen bonds : bond 0.03179 ( 178) hydrogen bonds : angle 6.02447 ( 408) link_NAG-ASN : bond 0.00329 ( 4) link_NAG-ASN : angle 2.46473 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 GLU cc_start: 0.8293 (tp30) cc_final: 0.7963 (tp30) REVERT: G 261 MET cc_start: 0.7611 (pmm) cc_final: 0.7330 (pmm) REVERT: G 275 ASN cc_start: 0.7568 (t0) cc_final: 0.7307 (t0) REVERT: G 340 ASP cc_start: 0.8151 (p0) cc_final: 0.7770 (p0) REVERT: H 278 GLU cc_start: 0.8725 (tp30) cc_final: 0.8449 (tp30) REVERT: H 340 ASP cc_start: 0.7726 (p0) cc_final: 0.7418 (p0) outliers start: 9 outliers final: 7 residues processed: 118 average time/residue: 0.2808 time to fit residues: 40.0117 Evaluate side-chains 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116521 restraints weight = 24547.134| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.58 r_work: 0.3369 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6539 Z= 0.145 Angle : 0.542 7.096 8884 Z= 0.280 Chirality : 0.050 0.391 988 Planarity : 0.004 0.060 1126 Dihedral : 9.196 94.266 958 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.18 % Allowed : 10.36 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.29), residues: 818 helix: 1.40 (0.93), residues: 34 sheet: -1.14 (0.32), residues: 266 loop : -1.31 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 332 TYR 0.015 0.002 TYR A 239 PHE 0.017 0.002 PHE G 225 TRP 0.007 0.001 TRP A 212 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6526) covalent geometry : angle 0.53098 ( 8854) SS BOND : bond 0.00468 ( 9) SS BOND : angle 1.39955 ( 18) hydrogen bonds : bond 0.03058 ( 178) hydrogen bonds : angle 5.99581 ( 408) link_NAG-ASN : bond 0.00352 ( 4) link_NAG-ASN : angle 2.53129 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 GLU cc_start: 0.7922 (mm-30) cc_final: 0.6707 (pm20) REVERT: B 350 GLU cc_start: 0.8297 (tp30) cc_final: 0.7981 (tp30) REVERT: G 261 MET cc_start: 0.7587 (pmm) cc_final: 0.7295 (pmm) REVERT: G 275 ASN cc_start: 0.7569 (t0) cc_final: 0.7310 (t0) REVERT: G 340 ASP cc_start: 0.8146 (p0) cc_final: 0.7767 (p0) REVERT: H 278 GLU cc_start: 0.8717 (tp30) cc_final: 0.8433 (tp30) REVERT: H 340 ASP cc_start: 0.7736 (p0) cc_final: 0.7428 (p0) outliers start: 8 outliers final: 6 residues processed: 118 average time/residue: 0.2464 time to fit residues: 35.1395 Evaluate side-chains 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116051 restraints weight = 24377.942| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.62 r_work: 0.3359 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6539 Z= 0.144 Angle : 0.547 7.216 8884 Z= 0.282 Chirality : 0.050 0.395 988 Planarity : 0.004 0.060 1126 Dihedral : 8.874 93.472 958 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.04 % Allowed : 10.50 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.29), residues: 818 helix: 1.41 (0.93), residues: 34 sheet: -1.17 (0.32), residues: 266 loop : -1.32 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 332 TYR 0.015 0.001 TYR A 239 PHE 0.016 0.002 PHE G 225 TRP 0.007 0.001 TRP A 212 HIS 0.005 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6526) covalent geometry : angle 0.53515 ( 8854) SS BOND : bond 0.00446 ( 9) SS BOND : angle 1.37549 ( 18) hydrogen bonds : bond 0.03057 ( 178) hydrogen bonds : angle 5.98126 ( 408) link_NAG-ASN : bond 0.00326 ( 4) link_NAG-ASN : angle 2.72397 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.83 seconds wall clock time: 53 minutes 16.57 seconds (3196.57 seconds total)