Starting phenix.real_space_refine on Sun Mar 10 14:32:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q96_18269/03_2024/8q96_18269_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q96_18269/03_2024/8q96_18269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q96_18269/03_2024/8q96_18269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q96_18269/03_2024/8q96_18269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q96_18269/03_2024/8q96_18269_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q96_18269/03_2024/8q96_18269_neut.pdb" } resolution = 3.09 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 1296 2.51 5 N 392 2.21 5 O 404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2100 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 415 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 415 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 415 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 415 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.92, per 1000 atoms: 0.91 Number of scatterers: 2100 At special positions: 0 Unit cell: (86.25, 77.05, 41.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 404 8.00 N 392 7.00 C 1296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 867.9 milliseconds 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 51.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 275 through 283 removed outlier: 8.946A pdb=" N GLN D 276 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N ASN J 279 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ILE D 278 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N LYS J 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS D 280 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP J 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU D 282 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN J 276 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 277 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE J 278 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 279 " --> pdb=" O ILE J 278 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS J 280 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS A 281 " --> pdb=" O LYS J 280 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N GLN A 276 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ASN G 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE A 278 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N LYS G 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A 280 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP G 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 282 " --> pdb=" O ASP G 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 286 through 287 removed outlier: 6.312A pdb=" N ASN D 286 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 286 " --> pdb=" O VAL G 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 292 through 302 removed outlier: 9.196A pdb=" N GLY D 292 " --> pdb=" O SER J 293 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N ASP J 295 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N LYS D 294 " --> pdb=" O ASP J 295 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N ILE J 297 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ASN D 296 " --> pdb=" O ILE J 297 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N HIS J 299 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS D 298 " --> pdb=" O HIS J 299 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER J 301 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 300 " --> pdb=" O SER J 301 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 293 " --> pdb=" O GLY J 292 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS J 294 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP A 295 " --> pdb=" O LYS J 294 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN J 296 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 297 " --> pdb=" O ASN J 296 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS J 298 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N GLY A 292 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP G 295 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N LYS A 294 " --> pdb=" O ASP G 295 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N ILE G 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ASN A 296 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N HIS G 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS A 298 " --> pdb=" O HIS G 299 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER G 301 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 300 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.538A pdb=" N GLN A 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N TYR J 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.903A pdb=" N VAL D 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.676A pdb=" N LYS D 317 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS A 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 323 through 327 removed outlier: 7.483A pdb=" N GLY D 323 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY J 326 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N LEU D 325 " --> pdb=" O GLY J 326 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU J 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY A 326 " --> pdb=" O LEU J 325 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN J 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLY A 323 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLY G 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N LEU A 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) 18 hydrogen bonds defined for protein. 54 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: 0.46 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 629 1.34 - 1.46: 427 1.46 - 1.58: 1040 1.58 - 1.70: 0 1.70 - 1.81: 8 Bond restraints: 2104 Sorted by residual: bond pdb=" CA SER A 289 " pdb=" CB SER A 289 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.83e-02 2.99e+03 9.57e+00 bond pdb=" CA SER G 289 " pdb=" CB SER G 289 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.83e-02 2.99e+03 9.56e+00 bond pdb=" CA SER D 289 " pdb=" CB SER D 289 " ideal model delta sigma weight residual 1.531 1.474 0.056 1.83e-02 2.99e+03 9.51e+00 bond pdb=" CA SER J 289 " pdb=" CB SER J 289 " ideal model delta sigma weight residual 1.531 1.475 0.056 1.83e-02 2.99e+03 9.39e+00 bond pdb=" CA SER G 324 " pdb=" CB SER G 324 " ideal model delta sigma weight residual 1.532 1.499 0.033 1.36e-02 5.41e+03 5.72e+00 ... (remaining 2099 not shown) Histogram of bond angle deviations from ideal: 101.82 - 107.56: 88 107.56 - 113.31: 1172 113.31 - 119.05: 537 119.05 - 124.80: 1011 124.80 - 130.55: 16 Bond angle restraints: 2824 Sorted by residual: angle pdb=" CA ASP D 283 " pdb=" CB ASP D 283 " pdb=" CG ASP D 283 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" CA ASP A 283 " pdb=" CB ASP A 283 " pdb=" CG ASP A 283 " ideal model delta sigma weight residual 112.60 116.36 -3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA ASP J 283 " pdb=" CB ASP J 283 " pdb=" CG ASP J 283 " ideal model delta sigma weight residual 112.60 116.35 -3.75 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA ASP G 283 " pdb=" CB ASP G 283 " pdb=" CG ASP G 283 " ideal model delta sigma weight residual 112.60 116.35 -3.75 1.00e+00 1.00e+00 1.41e+01 angle pdb=" N LYS D 321 " pdb=" CA LYS D 321 " pdb=" C LYS D 321 " ideal model delta sigma weight residual 110.48 106.08 4.40 1.48e+00 4.57e-01 8.85e+00 ... (remaining 2819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.98: 1028 6.98 - 13.97: 168 13.97 - 20.95: 64 20.95 - 27.94: 16 27.94 - 34.92: 20 Dihedral angle restraints: 1296 sinusoidal: 416 harmonic: 880 Sorted by residual: dihedral pdb=" CA UNK I 3 " pdb=" C UNK I 3 " pdb=" N UNK I 4 " pdb=" CA UNK I 4 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA UNK C 3 " pdb=" C UNK C 3 " pdb=" N UNK C 4 " pdb=" CA UNK C 4 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA UNK L 3 " pdb=" C UNK L 3 " pdb=" N UNK L 4 " pdb=" CA UNK L 4 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 127 0.036 - 0.072: 105 0.072 - 0.109: 60 0.109 - 0.145: 56 0.145 - 0.181: 8 Chirality restraints: 356 Sorted by residual: chirality pdb=" CA SER G 324 " pdb=" N SER G 324 " pdb=" C SER G 324 " pdb=" CB SER G 324 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA SER A 324 " pdb=" N SER A 324 " pdb=" C SER A 324 " pdb=" CB SER A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA SER J 324 " pdb=" N SER J 324 " pdb=" C SER J 324 " pdb=" CB SER J 324 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 353 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK F 4 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C UNK F 4 " 0.028 2.00e-02 2.50e+03 pdb=" O UNK F 4 " -0.011 2.00e-02 2.50e+03 pdb=" N UNK F 5 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK I 4 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C UNK I 4 " 0.028 2.00e-02 2.50e+03 pdb=" O UNK I 4 " -0.011 2.00e-02 2.50e+03 pdb=" N UNK I 5 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK C 4 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C UNK C 4 " 0.028 2.00e-02 2.50e+03 pdb=" O UNK C 4 " -0.011 2.00e-02 2.50e+03 pdb=" N UNK C 5 " -0.009 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 1071 3.00 - 3.48: 1964 3.48 - 3.95: 2984 3.95 - 4.43: 3360 4.43 - 4.90: 6453 Nonbonded interactions: 15832 Sorted by model distance: nonbonded pdb=" OD1 ASP G 314 " pdb=" OG SER G 316 " model vdw 2.529 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.529 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.529 2.440 nonbonded pdb=" OD1 ASP J 314 " pdb=" OG SER J 316 " model vdw 2.530 2.440 nonbonded pdb=" N LEU D 315 " pdb=" O ASP J 314 " model vdw 2.584 2.520 ... (remaining 15827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.000 Extract box with map and model: 2.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.160 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:2.740 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: 0.8286 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 : 0.009 0.057 2104 Z= 0.604 Angle : 1.243 5.048 2824 Z= 0.743 Chirality : 0.074 0.181 356 Planarity : 0.006 0.016 356 Dihedral : 10.143 34.921 720 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.37), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 299 TYR 0.007 0.004 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 288 GLN cc_start: 0.9234 (mt0) cc_final: 0.8934 (mt0) REVERT: D 321 LYS cc_start: 0.8410 (mttt) cc_final: 0.8114 (mtpp) REVERT: J 283 ASP cc_start: 0.8930 (t0) cc_final: 0.8717 (t0) REVERT: J 288 GLN cc_start: 0.9226 (mt0) cc_final: 0.9020 (mt0) REVERT: J 321 LYS cc_start: 0.8352 (mttt) cc_final: 0.8004 (mtpt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1985 time to fit residues: 14.6734 Evaluate side-chains 57 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2104 Z= 0.262 Angle : 0.618 7.241 2824 Z= 0.284 Chirality : 0.050 0.144 356 Planarity : 0.002 0.009 356 Dihedral : 5.272 18.701 304 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.50 % Allowed : 11.50 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.37), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.28), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 TYR 0.010 0.002 TYR G 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.238 Fit side-chains REVERT: A 288 GLN cc_start: 0.9270 (mt0) cc_final: 0.8985 (mt0) REVERT: D 321 LYS cc_start: 0.8456 (mttt) cc_final: 0.8199 (mtpp) REVERT: J 288 GLN cc_start: 0.9291 (mt0) cc_final: 0.9050 (mt0) REVERT: J 321 LYS cc_start: 0.8339 (mttt) cc_final: 0.8103 (mtpp) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.1848 time to fit residues: 12.0405 Evaluate side-chains 58 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 2104 Z= 0.535 Angle : 0.752 6.832 2824 Z= 0.357 Chirality : 0.053 0.157 356 Planarity : 0.003 0.013 356 Dihedral : 5.803 16.429 304 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.38), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 329 TYR 0.014 0.004 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.236 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1910 time to fit residues: 11.1613 Evaluate side-chains 53 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2104 Z= 0.277 Angle : 0.623 6.752 2824 Z= 0.290 Chirality : 0.049 0.165 356 Planarity : 0.002 0.012 356 Dihedral : 5.248 18.471 304 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.50 % Allowed : 16.00 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.39), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.009 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.235 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.2019 time to fit residues: 11.6838 Evaluate side-chains 55 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2104 Z= 0.349 Angle : 0.657 6.975 2824 Z= 0.303 Chirality : 0.049 0.163 356 Planarity : 0.002 0.013 356 Dihedral : 5.269 17.909 304 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.00 % Allowed : 15.00 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.40), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.009 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.257 Fit side-chains REVERT: J 295 ASP cc_start: 0.8626 (m-30) cc_final: 0.8364 (m-30) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.2057 time to fit residues: 11.7373 Evaluate side-chains 54 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 0.0040 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 overall best weight: 3.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2104 Z= 0.329 Angle : 0.675 8.427 2824 Z= 0.304 Chirality : 0.049 0.165 356 Planarity : 0.002 0.013 356 Dihedral : 5.255 18.552 304 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.50 % Allowed : 14.50 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.40), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.008 0.002 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.232 Fit side-chains REVERT: J 295 ASP cc_start: 0.8630 (m-30) cc_final: 0.8378 (m-30) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.2091 time to fit residues: 12.1474 Evaluate side-chains 56 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2104 Z= 0.255 Angle : 0.611 6.529 2824 Z= 0.281 Chirality : 0.049 0.166 356 Planarity : 0.002 0.012 356 Dihedral : 5.095 18.290 304 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.50 % Allowed : 14.50 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.41), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 299 TYR 0.007 0.002 TYR G 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.221 Fit side-chains REVERT: J 295 ASP cc_start: 0.8625 (m-30) cc_final: 0.8315 (m-30) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.2192 time to fit residues: 12.2346 Evaluate side-chains 51 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2104 Z= 0.310 Angle : 0.634 6.184 2824 Z= 0.291 Chirality : 0.049 0.166 356 Planarity : 0.002 0.012 356 Dihedral : 5.195 18.458 304 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.00 % Allowed : 15.00 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.41), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.32), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.008 0.002 TYR G 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.244 Fit side-chains REVERT: D 295 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: J 295 ASP cc_start: 0.8570 (m-30) cc_final: 0.8345 (m-30) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.2132 time to fit residues: 12.1630 Evaluate side-chains 55 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2104 Z= 0.242 Angle : 0.616 6.268 2824 Z= 0.279 Chirality : 0.049 0.165 356 Planarity : 0.002 0.012 356 Dihedral : 5.074 18.621 304 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.50 % Allowed : 16.00 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.42), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.32), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.007 0.002 TYR G 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.246 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 0.1986 time to fit residues: 11.0635 Evaluate side-chains 54 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 2104 Z= 0.449 Angle : 0.711 6.808 2824 Z= 0.328 Chirality : 0.051 0.177 356 Planarity : 0.002 0.014 356 Dihedral : 5.423 18.001 304 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.00 % Allowed : 16.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.42), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 TYR 0.011 0.003 TYR D 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.256 Fit side-chains REVERT: D 295 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: D 321 LYS cc_start: 0.8591 (mttt) cc_final: 0.8341 (mttt) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.2092 time to fit residues: 12.4004 Evaluate side-chains 55 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 ASN ** 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 = 0.3612 r_free = 0.3612 target = 0.106011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096412 restraints weight = 2955.630| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.00 r_work: 0.3380 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2104 Z= 0.236 Angle : 0.628 6.663 2824 Z= 0.285 Chirality : 0.049 0.167 356 Planarity : 0.002 0.013 356 Dihedral : 5.183 18.788 304 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.50 % Allowed : 17.50 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.42), residues: 216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.32), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 299 TYR 0.007 0.002 TYR G 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 842.33 seconds wall clock time: 15 minutes 50.83 seconds (950.83 seconds total)