Starting phenix.real_space_refine on Thu Dec 7 23:14:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izv_9758/12_2023/6izv_9758_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izv_9758/12_2023/6izv_9758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izv_9758/12_2023/6izv_9758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izv_9758/12_2023/6izv_9758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izv_9758/12_2023/6izv_9758_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izv_9758/12_2023/6izv_9758_updated.pdb" } resolution = 4.2 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= 0.011 sd= 0.077 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 3578 2.51 5 N 940 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 245": "NH1" <-> "NH2" Residue "1 ARG 245": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5624 Number of models: 1 Model: "" Number of chains: 4 Chain: "0" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "1" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.69, per 1000 atoms: 0.66 Number of scatterers: 5624 At special positions: 0 Unit cell: (73.205, 83.853, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 4 15.00 Mg 2 11.99 O 1080 8.00 N 940 7.00 C 3578 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: 2.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 10 sheets defined 33.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain '0' and resid 39 through 43 removed outlier: 3.648A pdb=" N PHE 0 43 " --> pdb=" O LEU 0 39 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 39 through 43' Processing helix chain '0' and resid 49 through 51 No H-bonds generated for 'chain '0' and resid 49 through 51' Processing helix chain '0' and resid 71 through 75 removed outlier: 3.525A pdb=" N ARG 0 75 " --> pdb=" O GLU 0 71 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 71 through 75' Processing helix chain '0' and resid 92 through 103 Processing helix chain '0' and resid 126 through 129 No H-bonds generated for 'chain '0' and resid 126 through 129' Processing helix chain '0' and resid 131 through 140 removed outlier: 3.683A pdb=" N LYS 0 139 " --> pdb=" O ASN 0 135 " (cutoff:3.500A) Processing helix chain '0' and resid 170 through 174 Processing helix chain '0' and resid 181 through 183 No H-bonds generated for 'chain '0' and resid 181 through 183' Processing helix chain '0' and resid 229 through 244 removed outlier: 3.883A pdb=" N ASN 0 234 " --> pdb=" O ASN 0 231 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET 0 236 " --> pdb=" O TYR 0 233 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP 0 237 " --> pdb=" O ASN 0 234 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR 0 241 " --> pdb=" O LYS 0 238 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP 0 242 " --> pdb=" O ALA 0 239 " (cutoff:3.500A) Processing helix chain '0' and resid 252 through 261 removed outlier: 3.697A pdb=" N CYS 0 259 " --> pdb=" O LEU 0 255 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU 0 260 " --> pdb=" O MET 0 256 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 0 261 " --> pdb=" O LEU 0 257 " (cutoff:3.500A) Processing helix chain '0' and resid 274 through 295 removed outlier: 4.358A pdb=" N LYS 0 291 " --> pdb=" O ASN 0 287 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU 0 295 " --> pdb=" O LYS 0 291 " (cutoff:3.500A) Processing helix chain '0' and resid 298 through 302 Processing helix chain '0' and resid 311 through 316 removed outlier: 3.809A pdb=" N VAL 0 315 " --> pdb=" O GLY 0 311 " (cutoff:3.500A) Processing helix chain '0' and resid 320 through 323 removed outlier: 3.575A pdb=" N ILE 0 323 " --> pdb=" O LEU 0 320 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 320 through 323' Processing helix chain '0' and resid 337 through 344 Processing helix chain '1' and resid 39 through 43 removed outlier: 3.649A pdb=" N PHE 1 43 " --> pdb=" O LEU 1 39 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 39 through 43' Processing helix chain '1' and resid 49 through 51 No H-bonds generated for 'chain '1' and resid 49 through 51' Processing helix chain '1' and resid 71 through 75 removed outlier: 3.524A pdb=" N ARG 1 75 " --> pdb=" O GLU 1 71 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 71 through 75' Processing helix chain '1' and resid 92 through 103 Processing helix chain '1' and resid 126 through 129 No H-bonds generated for 'chain '1' and resid 126 through 129' Processing helix chain '1' and resid 131 through 140 removed outlier: 3.684A pdb=" N LYS 1 139 " --> pdb=" O ASN 1 135 " (cutoff:3.500A) Processing helix chain '1' and resid 170 through 174 Processing helix chain '1' and resid 181 through 183 No H-bonds generated for 'chain '1' and resid 181 through 183' Processing helix chain '1' and resid 229 through 244 removed outlier: 3.885A pdb=" N ASN 1 234 " --> pdb=" O ASN 1 231 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET 1 236 " --> pdb=" O TYR 1 233 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP 1 237 " --> pdb=" O ASN 1 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR 1 241 " --> pdb=" O LYS 1 238 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP 1 242 " --> pdb=" O ALA 1 239 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 261 removed outlier: 3.697A pdb=" N CYS 1 259 " --> pdb=" O LEU 1 255 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU 1 260 " --> pdb=" O MET 1 256 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 1 261 " --> pdb=" O LEU 1 257 " (cutoff:3.500A) Processing helix chain '1' and resid 274 through 295 removed outlier: 4.359A pdb=" N LYS 1 291 " --> pdb=" O ASN 1 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 1 295 " --> pdb=" O LYS 1 291 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 302 Processing helix chain '1' and resid 311 through 316 removed outlier: 3.809A pdb=" N VAL 1 315 " --> pdb=" O GLY 1 311 " (cutoff:3.500A) Processing helix chain '1' and resid 320 through 323 removed outlier: 3.575A pdb=" N ILE 1 323 " --> pdb=" O LEU 1 320 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 320 through 323' Processing helix chain '1' and resid 337 through 344 Processing sheet with id= A, first strand: chain '0' and resid 24 through 28 removed outlier: 4.437A pdb=" N GLY 0 121 " --> pdb=" O ILE 0 8 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR 0 164 " --> pdb=" O THR 0 120 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU 0 122 " --> pdb=" O THR 0 164 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE 0 166 " --> pdb=" O LEU 0 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 31 through 33 removed outlier: 4.040A pdb=" N PHE 0 152 " --> pdb=" O PHE 0 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 222 through 224 removed outlier: 7.862A pdb=" N GLY 0 192 " --> pdb=" O ASN 0 304 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE 0 306 " --> pdb=" O GLY 0 192 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE 0 194 " --> pdb=" O ILE 0 306 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE 0 308 " --> pdb=" O ILE 0 194 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL 0 196 " --> pdb=" O ILE 0 308 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '0' and resid 206 through 208 Processing sheet with id= E, first strand: chain '0' and resid 263 through 265 removed outlier: 3.784A pdb=" N ILE 0 264 " --> pdb=" O ILE 0 271 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 24 through 28 removed outlier: 4.438A pdb=" N GLY 1 121 " --> pdb=" O ILE 1 8 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR 1 164 " --> pdb=" O THR 1 120 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU 1 122 " --> pdb=" O THR 1 164 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE 1 166 " --> pdb=" O LEU 1 122 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 31 through 33 removed outlier: 4.040A pdb=" N PHE 1 152 " --> pdb=" O PHE 1 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 222 through 224 removed outlier: 7.862A pdb=" N GLY 1 192 " --> pdb=" O ASN 1 304 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE 1 306 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE 1 194 " --> pdb=" O ILE 1 306 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE 1 308 " --> pdb=" O ILE 1 194 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL 1 196 " --> pdb=" O ILE 1 308 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1' and resid 206 through 208 Processing sheet with id= J, first strand: chain '1' and resid 263 through 265 removed outlier: 3.784A pdb=" N ILE 1 264 " --> pdb=" O ILE 1 271 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 432 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: 1.59 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1825 1.34 - 1.46: 1065 1.46 - 1.57: 2790 1.57 - 1.69: 6 1.69 - 1.80: 36 Bond restraints: 5722 Sorted by residual: bond pdb=" C ASN 0 162 " pdb=" N ILE 0 163 " ideal model delta sigma weight residual 1.334 1.316 0.018 1.29e-02 6.01e+03 1.92e+00 bond pdb=" C ASN 1 162 " pdb=" N ILE 1 163 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.81e+00 bond pdb=" C4 ADP 1 401 " pdb=" C5 ADP 1 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C4 ADP 0 401 " pdb=" C5 ADP 0 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CA VAL 1 196 " pdb=" CB VAL 1 196 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.36e+00 ... (remaining 5717 not shown) Histogram of bond angle deviations from ideal: 100.07 - 107.29: 157 107.29 - 114.51: 3385 114.51 - 121.73: 2883 121.73 - 128.95: 1267 128.95 - 136.17: 20 Bond angle restraints: 7712 Sorted by residual: angle pdb=" C SER 0 175 " pdb=" N LYS 0 176 " pdb=" CA LYS 0 176 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C SER 1 175 " pdb=" N LYS 1 176 " pdb=" CA LYS 1 176 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N ILE 0 83 " pdb=" CA ILE 0 83 " pdb=" C ILE 0 83 " ideal model delta sigma weight residual 113.42 109.34 4.08 1.17e+00 7.31e-01 1.22e+01 angle pdb=" N ILE 1 83 " pdb=" CA ILE 1 83 " pdb=" C ILE 1 83 " ideal model delta sigma weight residual 113.42 109.35 4.07 1.17e+00 7.31e-01 1.21e+01 angle pdb=" C PRO 0 325 " pdb=" N ASN 0 326 " pdb=" CA ASN 0 326 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 ... (remaining 7707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.87: 3412 29.87 - 59.74: 37 59.74 - 89.61: 8 89.61 - 119.48: 0 119.48 - 149.35: 1 Dihedral angle restraints: 3458 sinusoidal: 1446 harmonic: 2012 Sorted by residual: dihedral pdb=" O1B ADP 0 401 " pdb=" O3A ADP 0 401 " pdb=" PB ADP 0 401 " pdb=" PA ADP 0 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.64 149.35 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" CA CYS 0 259 " pdb=" C CYS 0 259 " pdb=" N GLU 0 260 " pdb=" CA GLU 0 260 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS 1 259 " pdb=" C CYS 1 259 " pdb=" N GLU 1 260 " pdb=" CA GLU 1 260 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 594 0.049 - 0.097: 205 0.097 - 0.146: 54 0.146 - 0.194: 3 0.194 - 0.242: 4 Chirality restraints: 860 Sorted by residual: chirality pdb=" CB VAL 0 55 " pdb=" CA VAL 0 55 " pdb=" CG1 VAL 0 55 " pdb=" CG2 VAL 0 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL 1 55 " pdb=" CA VAL 1 55 " pdb=" CG1 VAL 1 55 " pdb=" CG2 VAL 1 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE 0 26 " pdb=" CA ILE 0 26 " pdb=" CG1 ILE 0 26 " pdb=" CG2 ILE 0 26 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 857 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 0 345 " -0.016 2.00e-02 2.50e+03 1.85e-02 5.99e+00 pdb=" CG PHE 0 345 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 0 345 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE 0 345 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 0 345 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE 0 345 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE 0 345 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 345 " 0.016 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE 1 345 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 345 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 345 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 345 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 345 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE 1 345 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 1 148 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C VAL 1 148 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL 1 148 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP 1 149 " -0.011 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 214 2.72 - 3.26: 5457 3.26 - 3.81: 8834 3.81 - 4.35: 11160 4.35 - 4.90: 18581 Nonbonded interactions: 44246 Sorted by model distance: nonbonded pdb=" NE2 GLN 1 168 " pdb="MG MG 1 402 " model vdw 2.170 2.250 nonbonded pdb=" NE2 GLN 0 168 " pdb="MG MG 0 402 " model vdw 2.171 2.250 nonbonded pdb=" O1B ADP 1 401 " pdb="MG MG 1 402 " model vdw 2.265 2.170 nonbonded pdb=" O2B ADP 0 401 " pdb="MG MG 0 402 " model vdw 2.265 2.170 nonbonded pdb=" OH TYR 1 233 " pdb=" O2' ADP 1 401 " model vdw 2.281 2.440 ... (remaining 44241 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 '0' selection = chain '1' } 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 group one per residue 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: 0.060 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.380 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.005 0.031 5722 Z= 0.306 Angle : 0.899 8.642 7712 Z= 0.495 Chirality : 0.052 0.242 860 Planarity : 0.005 0.038 992 Dihedral : 10.554 149.352 2158 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -3.60 (0.28), residues: 694 helix: -3.74 (0.19), residues: 218 sheet: -2.24 (0.39), residues: 176 loop : -1.09 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP 0 296 HIS 0.007 0.002 HIS 1 54 PHE 0.038 0.003 PHE 0 345 TYR 0.010 0.002 TYR 1 270 ARG 0.003 0.001 ARG 0 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2174 time to fit residues: 56.5712 Evaluate side-chains 91 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN 0 94 ASN 0 135 ASN 0 150 HIS ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 94 ASN 1 150 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5722 Z= 0.317 Angle : 0.732 5.979 7712 Z= 0.380 Chirality : 0.049 0.330 860 Planarity : 0.004 0.032 992 Dihedral : 8.901 101.880 754 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.32 % Allowed : 3.54 % Favored : 96.14 % 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: -2.48 (0.30), residues: 694 helix: -2.23 (0.29), residues: 220 sheet: -1.90 (0.38), residues: 178 loop : -0.70 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 1 296 HIS 0.008 0.002 HIS 0 54 PHE 0.037 0.002 PHE 1 345 TYR 0.015 0.002 TYR 0 270 ARG 0.006 0.001 ARG 1 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.1700 time to fit residues: 26.5204 Evaluate side-chains 72 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN 0 52 ASN 0 94 ASN ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5722 Z= 0.268 Angle : 0.656 5.793 7712 Z= 0.338 Chirality : 0.045 0.149 860 Planarity : 0.004 0.028 992 Dihedral : 8.374 88.868 754 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -1.81 (0.32), residues: 694 helix: -1.39 (0.35), residues: 200 sheet: -1.76 (0.38), residues: 178 loop : -0.48 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 1 296 HIS 0.003 0.001 HIS 1 54 PHE 0.017 0.002 PHE 1 174 TYR 0.018 0.002 TYR 1 317 ARG 0.009 0.001 ARG 1 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.643 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: 100 average time/residue: 0.1488 time to fit residues: 20.4639 Evaluate side-chains 66 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN 0 94 ASN ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 319 HIS ** 1 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5722 Z= 0.352 Angle : 0.717 6.183 7712 Z= 0.367 Chirality : 0.046 0.148 860 Planarity : 0.004 0.033 992 Dihedral : 8.069 81.042 754 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: -1.71 (0.32), residues: 694 helix: -1.51 (0.33), residues: 214 sheet: -1.75 (0.38), residues: 178 loop : -0.13 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 1 296 HIS 0.005 0.001 HIS 0 319 PHE 0.022 0.002 PHE 1 345 TYR 0.020 0.002 TYR 1 317 ARG 0.004 0.001 ARG 1 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1686 time to fit residues: 21.4505 Evaluate side-chains 69 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 94 ASN ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5722 Z= 0.371 Angle : 0.732 7.055 7712 Z= 0.375 Chirality : 0.047 0.149 860 Planarity : 0.004 0.033 992 Dihedral : 8.006 78.470 754 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -1.65 (0.32), residues: 694 helix: -1.55 (0.32), residues: 216 sheet: -1.64 (0.39), residues: 178 loop : -0.06 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 1 296 HIS 0.005 0.002 HIS 0 143 PHE 0.021 0.002 PHE 1 345 TYR 0.023 0.002 TYR 1 317 ARG 0.007 0.001 ARG 1 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1494 time to fit residues: 18.6293 Evaluate side-chains 68 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 319 HIS ** 1 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5722 Z= 0.268 Angle : 0.661 7.212 7712 Z= 0.339 Chirality : 0.045 0.146 860 Planarity : 0.003 0.030 992 Dihedral : 7.615 74.519 754 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.40 (0.33), residues: 694 helix: -1.22 (0.34), residues: 210 sheet: -1.56 (0.42), residues: 152 loop : -0.16 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 1 296 HIS 0.004 0.001 HIS 1 54 PHE 0.029 0.002 PHE 0 345 TYR 0.021 0.002 TYR 1 317 ARG 0.004 0.001 ARG 1 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1585 time to fit residues: 20.2914 Evaluate side-chains 73 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 94 ASN ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5722 Z= 0.257 Angle : 0.655 6.588 7712 Z= 0.333 Chirality : 0.045 0.147 860 Planarity : 0.003 0.027 992 Dihedral : 7.337 70.837 754 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -1.20 (0.33), residues: 694 helix: -0.94 (0.35), residues: 206 sheet: -1.33 (0.41), residues: 162 loop : -0.17 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 1 296 HIS 0.004 0.001 HIS 1 54 PHE 0.022 0.002 PHE 0 345 TYR 0.023 0.002 TYR 1 317 ARG 0.003 0.001 ARG 1 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1574 time to fit residues: 20.8131 Evaluate side-chains 75 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 0.0050 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 218 GLN ** 1 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5722 Z= 0.179 Angle : 0.633 8.071 7712 Z= 0.320 Chirality : 0.045 0.163 860 Planarity : 0.003 0.028 992 Dihedral : 7.022 73.102 754 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.34), residues: 694 helix: -0.53 (0.38), residues: 194 sheet: -1.29 (0.42), residues: 162 loop : -0.14 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP 1 296 HIS 0.004 0.001 HIS 1 54 PHE 0.018 0.002 PHE 1 345 TYR 0.022 0.002 TYR 1 317 ARG 0.004 0.001 ARG 1 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1488 time to fit residues: 20.8717 Evaluate side-chains 70 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 94 ASN ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 14 GLN ** 1 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5722 Z= 0.358 Angle : 0.736 6.918 7712 Z= 0.377 Chirality : 0.047 0.166 860 Planarity : 0.004 0.026 992 Dihedral : 7.336 72.704 754 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -1.22 (0.33), residues: 694 helix: -0.99 (0.35), residues: 210 sheet: -1.43 (0.40), residues: 172 loop : -0.03 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 1 296 HIS 0.004 0.001 HIS 0 143 PHE 0.025 0.002 PHE 1 345 TYR 0.027 0.002 TYR 1 317 ARG 0.004 0.001 ARG 1 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1329 time to fit residues: 16.8362 Evaluate side-chains 73 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5722 Z= 0.192 Angle : 0.662 6.883 7712 Z= 0.337 Chirality : 0.046 0.151 860 Planarity : 0.003 0.034 992 Dihedral : 6.992 69.384 754 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.10 (0.33), residues: 694 helix: -0.64 (0.37), residues: 206 sheet: -1.23 (0.42), residues: 162 loop : -0.31 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 0 296 HIS 0.003 0.001 HIS 1 54 PHE 0.018 0.002 PHE 0 345 TYR 0.022 0.002 TYR 1 317 ARG 0.006 0.001 ARG 1 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1319 time to fit residues: 18.0551 Evaluate side-chains 73 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 135 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 150 HIS ** 1 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064733 restraints weight = 17458.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067080 restraints weight = 9925.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068723 restraints weight = 6616.728| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5722 Z= 0.216 Angle : 0.666 10.122 7712 Z= 0.338 Chirality : 0.045 0.147 860 Planarity : 0.003 0.037 992 Dihedral : 6.819 66.363 754 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -0.84 (0.34), residues: 694 helix: -0.36 (0.37), residues: 206 sheet: -1.08 (0.43), residues: 158 loop : -0.21 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP 1 296 HIS 0.003 0.001 HIS 1 54 PHE 0.019 0.002 PHE 1 345 TYR 0.023 0.002 TYR 1 317 ARG 0.003 0.001 ARG 1 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1236.21 seconds wall clock time: 23 minutes 30.63 seconds (1410.63 seconds total)