Starting phenix.real_space_refine on Thu Jul 2 08:28:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uer_64090/07_2026/9uer_64090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uer_64090/07_2026/9uer_64090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uer_64090/07_2026/9uer_64090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uer_64090/07_2026/9uer_64090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uer_64090/07_2026/9uer_64090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uer_64090/07_2026/9uer_64090.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 39 5.49 5 S 28 5.16 5 C 4814 2.51 5 N 1390 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7873 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "H" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 928 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "B" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 928 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 928 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 928 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1659 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 2 Chain: "F" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1702 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Time building chain proxies: 1.88, per 1000 atoms: 0.24 Number of scatterers: 7873 At special positions: 0 Unit cell: (75.84, 79.68, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 39 15.00 O 1602 8.00 N 1390 7.00 C 4814 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 412.2 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 60.3% alpha, 5.7% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.574A pdb=" N ARG A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 68 through 74 Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.506A pdb=" N ASP A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.876A pdb=" N LEU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 removed outlier: 3.604A pdb=" N LYS A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.574A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 68 through 74 Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.571A pdb=" N ASP B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.877A pdb=" N LEU B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 removed outlier: 3.603A pdb=" N LYS B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 27 through 46 removed outlier: 3.574A pdb=" N ARG C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 74 through 81 removed outlier: 3.570A pdb=" N ASP C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.877A pdb=" N LEU C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.603A pdb=" N LYS C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'D' and resid 14 through 24 Processing helix chain 'D' and resid 27 through 46 removed outlier: 3.573A pdb=" N ARG D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 74 through 81 removed outlier: 3.570A pdb=" N ASP D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.877A pdb=" N LEU D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.604A pdb=" N LYS D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 233 through 241 Processing helix chain 'E' and resid 244 through 262 removed outlier: 3.884A pdb=" N LEU E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 removed outlier: 4.235A pdb=" N ALA E 294 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 296 " --> pdb=" O ALA E 293 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 320 removed outlier: 4.277A pdb=" N ASN E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET E 320 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 351 removed outlier: 3.556A pdb=" N LEU E 346 " --> pdb=" O MET E 342 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP E 347 " --> pdb=" O ASN E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 51 through 57 Processing helix chain 'F' and resid 160 through 165 Processing helix chain 'F' and resid 171 through 175 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 247 through 262 removed outlier: 3.990A pdb=" N THR F 251 " --> pdb=" O LEU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 298 removed outlier: 3.858A pdb=" N ALA F 295 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN F 298 " --> pdb=" O ALA F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 325 Processing helix chain 'F' and resid 341 through 351 removed outlier: 4.032A pdb=" N VAL F 345 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 181 through 182 removed outlier: 3.610A pdb=" N CYS E 231 " --> pdb=" O GLN E 181 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP E 279 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 27 through 31 removed outlier: 4.255A pdb=" N LYS E 27 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 31 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.735A pdb=" N ILE F 5 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 232 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS F 231 " --> pdb=" O GLN F 181 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 181 " --> pdb=" O CYS F 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.668A pdb=" N VAL F 29 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.066A pdb=" N ALA F 185 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 279 through 283 removed outlier: 3.788A pdb=" N ALA F 280 " --> pdb=" O PHE F 333 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 331 " --> pdb=" O ALA F 282 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2100 1.33 - 1.45: 1609 1.45 - 1.57: 4266 1.57 - 1.69: 76 1.69 - 1.81: 42 Bond restraints: 8093 Sorted by residual: bond pdb=" C3' DG G 6 " pdb=" O3' DG G 6 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" P DT H 14 " pdb=" O5' DT H 14 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" C1' DC H 8 " pdb=" N1 DC H 8 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.72e+00 bond pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.19e-02 7.06e+03 9.35e+00 bond pdb=" C3' DT G 3 " pdb=" C2' DT G 3 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.39e+00 ... (remaining 8088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10332 1.62 - 3.24: 665 3.24 - 4.86: 108 4.86 - 6.48: 26 6.48 - 8.10: 12 Bond angle restraints: 11143 Sorted by residual: angle pdb=" O4' DG H 13 " pdb=" C4' DG H 13 " pdb=" C3' DG H 13 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.73e+01 angle pdb=" N3 DT G 1 " pdb=" C4 DT G 1 " pdb=" O4 DT G 1 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" C ASP E 287 " pdb=" N GLN E 288 " pdb=" CA GLN E 288 " ideal model delta sigma weight residual 120.68 127.30 -6.62 1.52e+00 4.33e-01 1.90e+01 angle pdb=" O5' DG H 13 " pdb=" C5' DG H 13 " pdb=" C4' DG H 13 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.81e+01 angle pdb=" N3 DT H 5 " pdb=" C4 DT H 5 " pdb=" O4 DT H 5 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 11138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.21: 4344 28.21 - 56.43: 441 56.43 - 84.64: 51 84.64 - 112.86: 1 112.86 - 141.07: 1 Dihedral angle restraints: 4838 sinusoidal: 2189 harmonic: 2649 Sorted by residual: dihedral pdb=" CA ASP F 233 " pdb=" C ASP F 233 " pdb=" N LYS F 234 " pdb=" CA LYS F 234 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ARG E 38 " pdb=" C ARG E 38 " pdb=" N ILE E 39 " pdb=" CA ILE E 39 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR F 3 " pdb=" C THR F 3 " pdb=" N PHE F 4 " pdb=" CA PHE F 4 " ideal model delta harmonic sigma weight residual 180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1192 0.105 - 0.210: 68 0.210 - 0.315: 1 0.315 - 0.420: 0 0.420 - 0.525: 7 Chirality restraints: 1268 Sorted by residual: chirality pdb=" P DC H 15 " pdb=" OP1 DC H 15 " pdb=" OP2 DC H 15 " pdb=" O5' DC H 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" P DT H 17 " pdb=" OP1 DT H 17 " pdb=" OP2 DT H 17 " pdb=" O5' DT H 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" P DT G 12 " pdb=" OP1 DT G 12 " pdb=" OP2 DT G 12 " pdb=" O5' DT G 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 1265 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 307 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP F 307 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP F 307 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL F 308 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 348 " -0.015 2.00e-02 2.50e+03 1.86e-02 6.02e+00 pdb=" CG PHE E 348 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 348 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E 348 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE E 348 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 348 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " -0.014 2.00e-02 2.50e+03 1.65e-02 5.42e+00 pdb=" CG TYR A 39 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 550 2.72 - 3.26: 7954 3.26 - 3.81: 13362 3.81 - 4.35: 15169 4.35 - 4.90: 24582 Nonbonded interactions: 61617 Sorted by model distance: nonbonded pdb=" N ASP A 53 " pdb=" OD1 ASP A 53 " model vdw 2.169 3.120 nonbonded pdb=" N ASP B 53 " pdb=" OD1 ASP B 53 " model vdw 2.169 3.120 nonbonded pdb=" N ASP D 53 " pdb=" OD1 ASP D 53 " model vdw 2.169 3.120 nonbonded pdb=" N ASP C 53 " pdb=" OD1 ASP C 53 " model vdw 2.170 3.120 nonbonded pdb=" OD2 ASP E 287 " pdb=" OH TYR E 324 " model vdw 2.212 3.040 ... (remaining 61612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 52 or resid 159 through 351)) } 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: 0.480 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 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 : 0.007 0.061 8093 Z= 0.412 Angle : 0.905 8.096 11143 Z= 0.577 Chirality : 0.063 0.525 1268 Planarity : 0.006 0.055 1329 Dihedral : 20.143 141.071 3112 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 10.47 % Allowed : 4.97 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.27), residues: 879 helix: -0.08 (0.24), residues: 463 sheet: -2.04 (0.53), residues: 77 loop : -1.67 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 317 TYR 0.041 0.004 TYR A 39 PHE 0.043 0.003 PHE E 348 TRP 0.019 0.002 TRP F 279 HIS 0.007 0.001 HIS F 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.41 ( 8093) covalent geometry : angle 0.90515 / 0.58 (11143) hydrogen bonds : bond 0.16483 / 16.11 ( 356) hydrogen bonds : angle 7.38863 / 9.93 ( 1018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6955 (mm110) REVERT: D 100 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: E 6 GLN cc_start: 0.6749 (mt0) cc_final: 0.6376 (mp10) REVERT: E 263 SER cc_start: 0.8178 (p) cc_final: 0.7387 (p) REVERT: E 279 TRP cc_start: 0.5638 (t60) cc_final: 0.5422 (t60) REVERT: E 312 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.7024 (mtt180) REVERT: E 317 ARG cc_start: 0.7062 (ptt90) cc_final: 0.6805 (ptt90) REVERT: E 342 MET cc_start: 0.5502 (ttt) cc_final: 0.5024 (ttt) REVERT: F 311 GLN cc_start: 0.7125 (mp10) cc_final: 0.6901 (mp-120) outliers start: 80 outliers final: 25 residues processed: 280 average time/residue: 0.1073 time to fit residues: 38.8192 Evaluate side-chains 160 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN B 33 ASN C 22 ASN C 34 ASN D 60 ASN E 6 GLN E 332 HIS F 42 GLN F 240 ASN F 327 GLN F 332 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.195178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149064 restraints weight = 13700.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.153149 restraints weight = 7714.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.155718 restraints weight = 5438.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157128 restraints weight = 4449.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158051 restraints weight = 3989.069| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8093 Z= 0.207 Angle : 0.804 9.554 11143 Z= 0.427 Chirality : 0.047 0.325 1268 Planarity : 0.006 0.051 1329 Dihedral : 19.547 146.049 1471 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 4.58 % Allowed : 14.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.26), residues: 879 helix: 0.20 (0.23), residues: 469 sheet: -2.37 (0.62), residues: 56 loop : -1.67 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 312 TYR 0.015 0.002 TYR E 324 PHE 0.026 0.003 PHE B 36 TRP 0.016 0.002 TRP F 279 HIS 0.005 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 8093) covalent geometry : angle 0.80373 / 0.43 (11143) hydrogen bonds : bond 0.05785 / 6.09 ( 356) hydrogen bonds : angle 5.13412 / 6.86 ( 1018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7674 (t0) cc_final: 0.7156 (t70) REVERT: B 53 ASP cc_start: 0.7717 (p0) cc_final: 0.6784 (p0) REVERT: B 59 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6933 (mm) REVERT: C 84 ASP cc_start: 0.7119 (p0) cc_final: 0.6543 (t0) REVERT: D 51 ASP cc_start: 0.7006 (p0) cc_final: 0.6693 (p0) REVERT: E 6 GLN cc_start: 0.6800 (mt0) cc_final: 0.6109 (mp10) REVERT: E 163 MET cc_start: 0.7523 (mmm) cc_final: 0.6938 (mmm) REVERT: E 182 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7423 (m) REVERT: E 190 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7816 (tp30) REVERT: E 288 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7309 (tm130) REVERT: E 317 ARG cc_start: 0.7238 (ptt90) cc_final: 0.6834 (ptt90) REVERT: F 311 GLN cc_start: 0.7149 (mp10) cc_final: 0.6423 (mp10) outliers start: 35 outliers final: 20 residues processed: 181 average time/residue: 0.0947 time to fit residues: 22.7568 Evaluate side-chains 157 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 3 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN E 6 GLN E 331 GLN ** E 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.189056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.146925 restraints weight = 13967.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.146418 restraints weight = 8277.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147808 restraints weight = 6203.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148687 restraints weight = 5507.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148806 restraints weight = 4953.531| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8093 Z= 0.211 Angle : 0.739 9.163 11143 Z= 0.396 Chirality : 0.044 0.221 1268 Planarity : 0.006 0.049 1329 Dihedral : 19.422 142.047 1439 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.31 % Rotamer: Outliers : 4.97 % Allowed : 16.62 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.27), residues: 879 helix: 0.45 (0.24), residues: 465 sheet: -2.27 (0.63), residues: 55 loop : -1.72 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 312 TYR 0.020 0.002 TYR F 229 PHE 0.016 0.003 PHE B 36 TRP 0.030 0.004 TRP E 279 HIS 0.011 0.002 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 ( 8093) covalent geometry : angle 0.73927 / 0.40 (11143) hydrogen bonds : bond 0.05517 / 5.66 ( 356) hydrogen bonds : angle 4.93244 / 6.78 ( 1018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7868 (t0) cc_final: 0.7255 (t70) REVERT: A 82 SER cc_start: 0.8493 (p) cc_final: 0.7951 (t) REVERT: B 53 ASP cc_start: 0.7947 (p0) cc_final: 0.7098 (p0) REVERT: C 99 CYS cc_start: 0.7707 (m) cc_final: 0.7384 (m) REVERT: D 59 LEU cc_start: 0.8437 (tp) cc_final: 0.8234 (tt) REVERT: E 163 MET cc_start: 0.7769 (mmm) cc_final: 0.7206 (mmm) REVERT: E 182 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7386 (m) REVERT: E 190 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7853 (tp30) REVERT: E 288 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7311 (tm130) REVERT: E 317 ARG cc_start: 0.7156 (ptt90) cc_final: 0.6610 (ptt90) REVERT: E 331 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: F 312 ARG cc_start: 0.7338 (tpm170) cc_final: 0.6738 (tpm170) REVERT: F 336 MET cc_start: 0.0481 (OUTLIER) cc_final: 0.0217 (mpt) outliers start: 38 outliers final: 24 residues processed: 167 average time/residue: 0.0914 time to fit residues: 20.5454 Evaluate side-chains 153 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 336 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.189632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.148682 restraints weight = 14079.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147477 restraints weight = 7856.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.148843 restraints weight = 6143.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.150064 restraints weight = 5411.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.150133 restraints weight = 4826.403| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8093 Z= 0.157 Angle : 0.678 8.211 11143 Z= 0.361 Chirality : 0.043 0.197 1268 Planarity : 0.006 0.058 1329 Dihedral : 19.296 135.143 1436 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.84 % Allowed : 18.59 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 879 helix: 0.76 (0.24), residues: 465 sheet: -2.02 (0.64), residues: 55 loop : -1.69 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 312 TYR 0.021 0.002 TYR F 229 PHE 0.015 0.002 PHE B 36 TRP 0.009 0.001 TRP F 279 HIS 0.005 0.002 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 8093) covalent geometry : angle 0.67765 / 0.36 (11143) hydrogen bonds : bond 0.04821 / 4.99 ( 356) hydrogen bonds : angle 4.63449 / 6.34 ( 1018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7952 (t0) cc_final: 0.7210 (t0) REVERT: A 82 SER cc_start: 0.8449 (p) cc_final: 0.8035 (t) REVERT: B 44 ARG cc_start: 0.8374 (tmm-80) cc_final: 0.7964 (ttp80) REVERT: B 53 ASP cc_start: 0.7896 (p0) cc_final: 0.7136 (p0) REVERT: B 59 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7203 (mm) REVERT: B 63 ASN cc_start: 0.8242 (t0) cc_final: 0.7950 (m-40) REVERT: C 51 ASP cc_start: 0.7334 (t0) cc_final: 0.7128 (t0) REVERT: C 99 CYS cc_start: 0.7640 (m) cc_final: 0.7363 (m) REVERT: D 44 ARG cc_start: 0.7615 (mmp80) cc_final: 0.7018 (ttp80) REVERT: E 6 GLN cc_start: 0.7019 (mt0) cc_final: 0.6209 (mp10) REVERT: E 9 LEU cc_start: 0.6938 (mm) cc_final: 0.6732 (mp) REVERT: E 163 MET cc_start: 0.7762 (mmm) cc_final: 0.7240 (mmm) REVERT: E 182 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7442 (m) REVERT: E 190 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7858 (tp30) REVERT: E 288 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7400 (tm130) REVERT: E 317 ARG cc_start: 0.7381 (ptt90) cc_final: 0.7076 (ptt90) outliers start: 37 outliers final: 23 residues processed: 164 average time/residue: 0.0907 time to fit residues: 19.7851 Evaluate side-chains 150 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.184086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141517 restraints weight = 14031.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141092 restraints weight = 7623.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141584 restraints weight = 6765.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.142334 restraints weight = 5909.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142509 restraints weight = 5306.096| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8093 Z= 0.247 Angle : 0.771 8.113 11143 Z= 0.407 Chirality : 0.046 0.188 1268 Planarity : 0.006 0.058 1329 Dihedral : 19.301 132.564 1432 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.50 % Allowed : 18.06 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 879 helix: 0.53 (0.24), residues: 465 sheet: -2.17 (0.63), residues: 56 loop : -1.80 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 38 TYR 0.021 0.003 TYR E 324 PHE 0.027 0.003 PHE B 11 TRP 0.009 0.002 TRP F 279 HIS 0.007 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 ( 8093) covalent geometry : angle 0.77105 / 0.41 (11143) hydrogen bonds : bond 0.05879 / 6.17 ( 356) hydrogen bonds : angle 4.87426 / 6.76 ( 1018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 SER cc_start: 0.9112 (m) cc_final: 0.8718 (t) REVERT: A 81 ASP cc_start: 0.8083 (t0) cc_final: 0.7437 (t0) REVERT: A 82 SER cc_start: 0.8411 (p) cc_final: 0.8189 (t) REVERT: B 53 ASP cc_start: 0.8038 (p0) cc_final: 0.7330 (p0) REVERT: B 59 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7445 (mm) REVERT: B 60 ASN cc_start: 0.8636 (t0) cc_final: 0.7986 (t0) REVERT: B 63 ASN cc_start: 0.8317 (t0) cc_final: 0.8035 (m-40) REVERT: C 51 ASP cc_start: 0.7394 (t0) cc_final: 0.7123 (t0) REVERT: D 68 GLU cc_start: 0.8024 (mp0) cc_final: 0.7748 (mp0) REVERT: E 190 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8014 (tp30) REVERT: E 286 THR cc_start: 0.7228 (OUTLIER) cc_final: 0.6954 (m) REVERT: E 288 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7563 (tm130) REVERT: E 317 ARG cc_start: 0.7423 (ptt90) cc_final: 0.6752 (tmm-80) REVERT: F 189 SER cc_start: 0.7561 (t) cc_final: 0.7346 (p) outliers start: 42 outliers final: 28 residues processed: 169 average time/residue: 0.0856 time to fit residues: 19.4456 Evaluate side-chains 153 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 350 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 0.0270 chunk 2 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.188333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.145798 restraints weight = 13884.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145900 restraints weight = 7465.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147463 restraints weight = 5846.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148142 restraints weight = 5082.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148193 restraints weight = 4682.101| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8093 Z= 0.140 Angle : 0.673 7.807 11143 Z= 0.355 Chirality : 0.042 0.194 1268 Planarity : 0.005 0.048 1329 Dihedral : 19.046 129.083 1430 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 20.81 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.28), residues: 879 helix: 0.87 (0.24), residues: 464 sheet: -1.95 (0.56), residues: 66 loop : -1.73 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 312 TYR 0.016 0.002 TYR E 324 PHE 0.016 0.002 PHE D 36 TRP 0.009 0.001 TRP F 279 HIS 0.004 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 8093) covalent geometry : angle 0.67296 / 0.35 (11143) hydrogen bonds : bond 0.04550 / 4.71 ( 356) hydrogen bonds : angle 4.47626 / 6.20 ( 1018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 SER cc_start: 0.9006 (m) cc_final: 0.8627 (t) REVERT: A 28 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7557 (p) REVERT: A 44 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7751 (ptp90) REVERT: A 79 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7599 (tp) REVERT: A 81 ASP cc_start: 0.8097 (t0) cc_final: 0.7384 (t0) REVERT: A 82 SER cc_start: 0.8267 (p) cc_final: 0.7973 (t) REVERT: B 59 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7114 (mm) REVERT: B 60 ASN cc_start: 0.8534 (t0) cc_final: 0.7917 (t0) REVERT: B 63 ASN cc_start: 0.8347 (t0) cc_final: 0.8059 (m-40) REVERT: C 51 ASP cc_start: 0.7412 (t0) cc_final: 0.7155 (t0) REVERT: D 44 ARG cc_start: 0.7326 (mmp80) cc_final: 0.6784 (ttp80) REVERT: E 6 GLN cc_start: 0.6975 (mt0) cc_final: 0.5852 (mp-120) REVERT: E 163 MET cc_start: 0.7750 (mpp) cc_final: 0.7530 (mpp) REVERT: E 190 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7899 (tp30) REVERT: E 286 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6938 (m) REVERT: E 288 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7412 (tm130) REVERT: E 317 ARG cc_start: 0.7555 (ptt90) cc_final: 0.6942 (tmm-80) outliers start: 28 outliers final: 17 residues processed: 152 average time/residue: 0.0955 time to fit residues: 19.0495 Evaluate side-chains 144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN E 42 GLN ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.187644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.145494 restraints weight = 14023.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145656 restraints weight = 7549.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146669 restraints weight = 5722.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.147003 restraints weight = 5242.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.148199 restraints weight = 4888.233| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8093 Z= 0.139 Angle : 0.669 10.694 11143 Z= 0.345 Chirality : 0.041 0.181 1268 Planarity : 0.005 0.048 1329 Dihedral : 18.970 124.767 1428 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.93 % Allowed : 21.73 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.28), residues: 879 helix: 1.01 (0.25), residues: 471 sheet: -1.63 (0.57), residues: 66 loop : -1.90 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 312 TYR 0.017 0.002 TYR E 324 PHE 0.014 0.002 PHE A 36 TRP 0.012 0.002 TRP E 279 HIS 0.003 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8093) covalent geometry : angle 0.66903 / 0.35 (11143) hydrogen bonds : bond 0.04322 / 4.55 ( 356) hydrogen bonds : angle 4.38945 / 6.12 ( 1018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 SER cc_start: 0.9062 (m) cc_final: 0.8661 (t) REVERT: A 28 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7540 (p) REVERT: A 44 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7734 (ptp90) REVERT: A 79 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7602 (tp) REVERT: A 81 ASP cc_start: 0.8160 (t0) cc_final: 0.7458 (t0) REVERT: A 82 SER cc_start: 0.8312 (p) cc_final: 0.7988 (t) REVERT: B 53 ASP cc_start: 0.8161 (p0) cc_final: 0.7234 (p0) REVERT: B 59 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7269 (mm) REVERT: B 60 ASN cc_start: 0.8501 (t0) cc_final: 0.7886 (t0) REVERT: B 63 ASN cc_start: 0.8287 (t0) cc_final: 0.7999 (m-40) REVERT: C 51 ASP cc_start: 0.7428 (t0) cc_final: 0.7179 (t0) REVERT: D 44 ARG cc_start: 0.7275 (mmp80) cc_final: 0.6748 (ttp80) REVERT: D 68 GLU cc_start: 0.7737 (mp0) cc_final: 0.7489 (mp0) REVERT: E 163 MET cc_start: 0.7648 (mpp) cc_final: 0.7412 (mpp) REVERT: E 190 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7832 (tp30) REVERT: E 288 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7442 (tm130) REVERT: E 317 ARG cc_start: 0.7415 (ptt90) cc_final: 0.6896 (tmm-80) REVERT: E 336 MET cc_start: 0.4966 (ppp) cc_final: 0.4561 (ppp) REVERT: F 290 ARG cc_start: 0.7894 (ptt90) cc_final: 0.7042 (ptt-90) outliers start: 30 outliers final: 20 residues processed: 152 average time/residue: 0.0835 time to fit residues: 16.8085 Evaluate side-chains 145 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 11 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.187331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.144962 restraints weight = 13970.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.145005 restraints weight = 7493.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.146420 restraints weight = 5826.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147260 restraints weight = 5178.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147528 restraints weight = 4755.861| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8093 Z= 0.145 Angle : 0.669 9.238 11143 Z= 0.349 Chirality : 0.041 0.181 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.962 123.478 1428 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.53 % Allowed : 21.86 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 879 helix: 1.02 (0.25), residues: 465 sheet: -1.39 (0.64), residues: 56 loop : -1.77 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 312 TYR 0.017 0.001 TYR E 324 PHE 0.018 0.002 PHE F 186 TRP 0.007 0.002 TRP E 279 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8093) covalent geometry : angle 0.66937 / 0.35 (11143) hydrogen bonds : bond 0.04261 / 4.49 ( 356) hydrogen bonds : angle 4.37425 / 6.06 ( 1018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 SER cc_start: 0.9061 (m) cc_final: 0.8683 (t) REVERT: A 28 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7584 (p) REVERT: A 44 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7703 (ptp90) REVERT: A 79 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7649 (tp) REVERT: A 81 ASP cc_start: 0.8238 (t0) cc_final: 0.7455 (t0) REVERT: A 82 SER cc_start: 0.8266 (p) cc_final: 0.7966 (t) REVERT: B 59 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7221 (mm) REVERT: B 60 ASN cc_start: 0.8523 (t0) cc_final: 0.7916 (t0) REVERT: B 63 ASN cc_start: 0.8322 (t0) cc_final: 0.8046 (m-40) REVERT: C 51 ASP cc_start: 0.7584 (t0) cc_final: 0.7349 (t0) REVERT: C 85 TYR cc_start: 0.6919 (t80) cc_final: 0.6521 (t80) REVERT: D 44 ARG cc_start: 0.7291 (mmp80) cc_final: 0.6726 (ttp80) REVERT: E 163 MET cc_start: 0.7552 (mpp) cc_final: 0.7305 (mpp) REVERT: E 190 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7855 (tp30) REVERT: E 286 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.6911 (m) REVERT: E 288 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7421 (tm130) REVERT: E 317 ARG cc_start: 0.7448 (ptt90) cc_final: 0.6937 (tmm-80) REVERT: E 336 MET cc_start: 0.4856 (ppp) cc_final: 0.4398 (ppp) REVERT: F 311 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7492 (mm-40) outliers start: 27 outliers final: 17 residues processed: 150 average time/residue: 0.0949 time to fit residues: 18.8203 Evaluate side-chains 144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 311 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 22 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.185433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.144158 restraints weight = 13916.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.143410 restraints weight = 7417.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.144622 restraints weight = 5886.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.145026 restraints weight = 5612.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.145105 restraints weight = 5152.221| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8093 Z= 0.173 Angle : 0.697 9.396 11143 Z= 0.363 Chirality : 0.042 0.179 1268 Planarity : 0.005 0.049 1329 Dihedral : 19.010 123.067 1428 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.40 % Allowed : 21.99 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.27), residues: 879 helix: 0.95 (0.24), residues: 469 sheet: -1.37 (0.65), residues: 56 loop : -1.99 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 312 TYR 0.019 0.002 TYR E 324 PHE 0.018 0.002 PHE F 186 TRP 0.009 0.002 TRP E 279 HIS 0.005 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8093) covalent geometry : angle 0.69746 / 0.36 (11143) hydrogen bonds : bond 0.04536 / 4.77 ( 356) hydrogen bonds : angle 4.48478 / 6.17 ( 1018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 23 SER cc_start: 0.9144 (m) cc_final: 0.8768 (t) REVERT: A 28 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7676 (p) REVERT: A 44 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7630 (ptp90) REVERT: A 79 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 81 ASP cc_start: 0.8298 (t0) cc_final: 0.7535 (t0) REVERT: B 59 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7374 (mm) REVERT: B 60 ASN cc_start: 0.8596 (t0) cc_final: 0.7979 (t0) REVERT: B 63 ASN cc_start: 0.8366 (t0) cc_final: 0.8092 (m-40) REVERT: B 83 ASP cc_start: 0.8020 (t70) cc_final: 0.7804 (t70) REVERT: C 51 ASP cc_start: 0.7608 (t0) cc_final: 0.7372 (t0) REVERT: C 85 TYR cc_start: 0.6942 (t80) cc_final: 0.6502 (t80) REVERT: D 44 ARG cc_start: 0.7408 (mmp80) cc_final: 0.6851 (ttp80) REVERT: E 167 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.3663 (tmm) REVERT: E 190 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7913 (tp30) REVERT: E 286 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6907 (m) REVERT: E 288 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7394 (tm130) REVERT: E 317 ARG cc_start: 0.7407 (ptt90) cc_final: 0.7025 (tmm-80) REVERT: E 336 MET cc_start: 0.4792 (ppp) cc_final: 0.4323 (ppp) REVERT: F 290 ARG cc_start: 0.7800 (ptt90) cc_final: 0.7067 (ptt-90) REVERT: F 311 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7474 (mm-40) REVERT: F 312 ARG cc_start: 0.7703 (tpm170) cc_final: 0.6867 (tpm170) REVERT: F 326 GLN cc_start: 0.5331 (pm20) cc_final: 0.3778 (pt0) outliers start: 26 outliers final: 18 residues processed: 146 average time/residue: 0.0984 time to fit residues: 18.7803 Evaluate side-chains 146 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 311 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.185392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.143507 restraints weight = 13850.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142004 restraints weight = 7358.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.143532 restraints weight = 5740.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143951 restraints weight = 5283.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144014 restraints weight = 4794.570| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8093 Z= 0.171 Angle : 0.714 9.576 11143 Z= 0.371 Chirality : 0.043 0.319 1268 Planarity : 0.005 0.048 1329 Dihedral : 19.004 122.911 1428 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.40 % Allowed : 22.38 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.27), residues: 879 helix: 0.93 (0.24), residues: 467 sheet: -1.49 (0.57), residues: 66 loop : -1.99 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 312 TYR 0.019 0.002 TYR E 324 PHE 0.017 0.002 PHE F 186 TRP 0.008 0.002 TRP E 279 HIS 0.005 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 8093) covalent geometry : angle 0.71440 / 0.37 (11143) hydrogen bonds : bond 0.04526 / 4.76 ( 356) hydrogen bonds : angle 4.49083 / 6.16 ( 1018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 23 SER cc_start: 0.9152 (m) cc_final: 0.8788 (t) REVERT: A 28 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7674 (p) REVERT: A 44 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7633 (ptp90) REVERT: A 79 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7786 (tp) REVERT: A 81 ASP cc_start: 0.8343 (t0) cc_final: 0.7556 (t0) REVERT: B 59 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7378 (mm) REVERT: B 60 ASN cc_start: 0.8623 (t0) cc_final: 0.7990 (t0) REVERT: B 63 ASN cc_start: 0.8322 (t0) cc_final: 0.8077 (m-40) REVERT: B 83 ASP cc_start: 0.8035 (t70) cc_final: 0.7821 (t70) REVERT: C 51 ASP cc_start: 0.7654 (t0) cc_final: 0.7404 (t0) REVERT: D 44 ARG cc_start: 0.7372 (mmp80) cc_final: 0.6829 (ttp80) REVERT: E 163 MET cc_start: 0.7356 (mpp) cc_final: 0.7021 (mpp) REVERT: E 167 MET cc_start: 0.4119 (OUTLIER) cc_final: 0.3694 (mmm) REVERT: E 190 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7906 (tp30) REVERT: E 286 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6913 (m) REVERT: E 288 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7338 (tm130) REVERT: E 317 ARG cc_start: 0.7374 (ptt90) cc_final: 0.7027 (tmm-80) REVERT: E 336 MET cc_start: 0.4706 (ppp) cc_final: 0.4294 (ppp) REVERT: F 163 MET cc_start: 0.6134 (mmp) cc_final: 0.5858 (mmp) REVERT: F 290 ARG cc_start: 0.7687 (ptt90) cc_final: 0.6958 (ptt-90) REVERT: F 311 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7509 (mm-40) REVERT: F 312 ARG cc_start: 0.7852 (tpm170) cc_final: 0.7354 (tpm170) REVERT: F 326 GLN cc_start: 0.5352 (pm20) cc_final: 0.3779 (pt0) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 0.0846 time to fit residues: 16.0747 Evaluate side-chains 146 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 311 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145501 restraints weight = 13865.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145779 restraints weight = 7362.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147976 restraints weight = 5591.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148019 restraints weight = 4887.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.148212 restraints weight = 4598.506| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8093 Z= 0.135 Angle : 0.698 9.842 11143 Z= 0.363 Chirality : 0.041 0.193 1268 Planarity : 0.005 0.048 1329 Dihedral : 18.921 120.703 1428 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.88 % Allowed : 22.77 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.28), residues: 879 helix: 1.16 (0.25), residues: 460 sheet: -1.24 (0.58), residues: 64 loop : -1.80 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 38 TYR 0.015 0.001 TYR E 324 PHE 0.020 0.002 PHE F 4 TRP 0.008 0.002 TRP E 279 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 8093) covalent geometry : angle 0.69833 / 0.36 (11143) hydrogen bonds : bond 0.04044 / 4.26 ( 356) hydrogen bonds : angle 4.40390 / 5.98 ( 1018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.87 seconds wall clock time: 23 minutes 45.17 seconds (1425.17 seconds total)