Starting phenix.real_space_refine on Wed Aug 5 00:52:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uer_64090/08_2026/9uer_64090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uer_64090/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9uer_64090/08_2026/9uer_64090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uer_64090/08_2026/9uer_64090.map" model { file = "/net/cci-nas-00/data/ceres_data/9uer_64090/08_2026/9uer_64090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uer_64090/08_2026/9uer_64090.cif" } 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-2.2rc3-6140/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: 1.68, per 1000 atoms: 0.21 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: 0.78 Conformation dependent library (CDL) restraints added in 415.7 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: 0.80 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: 0.90 Time building geometry restraints manager: 1.00 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=" C3' DG H 13 " pdb=" O3' DG H 13 " pdb=" P DT H 14 " ideal model delta sigma weight residual 119.70 124.85 -5.15 1.20e+00 6.94e-01 1.84e+01 angle pdb=" C3' DC G 11 " pdb=" O3' DC G 11 " pdb=" P DT G 12 " ideal model delta sigma weight residual 119.70 114.58 5.12 1.20e+00 6.94e-01 1.82e+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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.470 Find NCS groups from input model: 0.080 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- 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= 0.579 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 0.90461 / 0.58 (11143) hydrogen bonds : bond 0.16483 / 16.28 ( 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 : 0.285 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: 0.6375 (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: 0.6806 (ptt90) REVERT: E 342 MET cc_start: 0.5502 (ttt) cc_final: 0.5025 (ttt) REVERT: F 311 GLN cc_start: 0.7125 (mp10) cc_final: 0.6902 (mp-120) outliers start: 80 outliers final: 26 residues processed: 280 average time/residue: 0.1083 time to fit residues: 39.2312 Evaluate side-chains 161 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 288 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN 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 = 0.4510 r_free = 0.4510 target = 0.193552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148364 restraints weight = 13981.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152473 restraints weight = 7739.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.155108 restraints weight = 5438.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.156175 restraints weight = 4449.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.157328 restraints weight = 4024.626| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8093 Z= 0.203 Angle : 0.799 9.938 11143 Z= 0.424 Chirality : 0.047 0.326 1268 Planarity : 0.006 0.050 1329 Dihedral : 19.563 145.123 1474 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.65 % Rotamer: Outliers : 4.58 % Allowed : 15.18 % Favored : 80.24 % 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: -1.08 (0.26), residues: 879 helix: 0.21 (0.23), residues: 470 sheet: -2.32 (0.63), residues: 56 loop : -1.65 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 253 TYR 0.016 0.002 TYR E 324 PHE 0.026 0.003 PHE B 36 TRP 0.016 0.002 TRP F 279 HIS 0.005 0.001 HIS E 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 ( 8093) covalent geometry : angle 0.79871 / 0.42 (11143) hydrogen bonds : bond 0.05875 / 6.21 ( 356) hydrogen bonds : angle 5.15956 / 6.90 ( 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 191 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7660 (t0) cc_final: 0.7148 (t70) REVERT: B 53 ASP cc_start: 0.7716 (p0) cc_final: 0.6782 (p0) REVERT: B 59 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7044 (mm) REVERT: C 84 ASP cc_start: 0.7082 (p0) cc_final: 0.6496 (t0) REVERT: D 51 ASP cc_start: 0.6998 (p0) cc_final: 0.6686 (p0) REVERT: E 6 GLN cc_start: 0.6769 (mt0) cc_final: 0.6052 (mp10) REVERT: E 163 MET cc_start: 0.7518 (mmm) cc_final: 0.6933 (mmm) REVERT: E 182 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7475 (m) REVERT: E 190 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7813 (tp30) REVERT: E 288 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7322 (tm130) REVERT: E 317 ARG cc_start: 0.7229 (ptt90) cc_final: 0.6814 (ptt90) REVERT: F 311 GLN cc_start: 0.7163 (mp10) cc_final: 0.6437 (mp10) outliers start: 35 outliers final: 22 residues processed: 180 average time/residue: 0.1010 time to fit residues: 23.9790 Evaluate side-chains 160 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 E residue 336 MET Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 336 MET 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: 5.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.188319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.145786 restraints weight = 13942.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145537 restraints weight = 7658.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147053 restraints weight = 5833.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147419 restraints weight = 5316.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.147534 restraints weight = 4947.525| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3475 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= 0.208 Angle : 0.749 9.649 11143 Z= 0.399 Chirality : 0.045 0.235 1268 Planarity : 0.006 0.049 1329 Dihedral : 19.438 140.932 1439 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.35 % Favored : 94.54 % Rotamer: Outliers : 4.97 % Allowed : 16.36 % Favored : 78.66 % 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: -0.97 (0.27), residues: 879 helix: 0.42 (0.24), residues: 464 sheet: -2.33 (0.62), residues: 55 loop : -1.75 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 312 TYR 0.021 0.002 TYR F 229 PHE 0.018 0.003 PHE B 11 TRP 0.017 0.003 TRP E 279 HIS 0.018 0.002 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 ( 8093) covalent geometry : angle 0.74930 / 0.40 (11143) hydrogen bonds : bond 0.05606 / 5.75 ( 356) hydrogen bonds : angle 4.93596 / 6.79 ( 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 181 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7876 (t0) cc_final: 0.7303 (t70) REVERT: B 53 ASP cc_start: 0.7955 (p0) cc_final: 0.7114 (p0) REVERT: D 59 LEU cc_start: 0.8435 (tp) cc_final: 0.8233 (tt) REVERT: E 6 GLN cc_start: 0.7060 (mt0) cc_final: 0.6856 (mt0) REVERT: E 163 MET cc_start: 0.7798 (mmm) cc_final: 0.7264 (mmm) REVERT: E 182 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7398 (m) REVERT: E 190 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7851 (tp30) REVERT: E 288 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7329 (tm130) REVERT: E 312 ARG cc_start: 0.7029 (mtt-85) cc_final: 0.6766 (mtt-85) REVERT: E 317 ARG cc_start: 0.7132 (ptt90) cc_final: 0.6616 (ptt90) REVERT: E 331 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: F 189 SER cc_start: 0.7596 (t) cc_final: 0.7329 (p) REVERT: F 312 ARG cc_start: 0.7260 (tpm170) cc_final: 0.6603 (tpm170) outliers start: 38 outliers final: 23 residues processed: 170 average time/residue: 0.0927 time to fit residues: 21.2590 Evaluate side-chains 153 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 335 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 308 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 40.0000 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN C 20 HIS ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.189992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.148245 restraints weight = 14107.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148036 restraints weight = 7925.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.150306 restraints weight = 5899.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150294 restraints weight = 5205.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150530 restraints weight = 4796.702| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3752 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= 0.143 Angle : 0.672 8.309 11143 Z= 0.354 Chirality : 0.042 0.215 1268 Planarity : 0.005 0.050 1329 Dihedral : 19.230 134.455 1432 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.45 % Allowed : 18.46 % Favored : 77.09 % 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: 0.75 (0.24), residues: 465 sheet: -2.06 (0.62), residues: 55 loop : -1.66 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 312 TYR 0.020 0.001 TYR F 229 PHE 0.015 0.002 PHE B 36 TRP 0.009 0.001 TRP F 279 HIS 0.006 0.002 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8093) covalent geometry : angle 0.67167 / 0.35 (11143) hydrogen bonds : bond 0.04706 / 4.87 ( 356) hydrogen bonds : angle 4.59652 / 6.32 ( 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 167 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7916 (t0) cc_final: 0.7418 (t70) REVERT: B 44 ARG cc_start: 0.8272 (tmm-80) cc_final: 0.7869 (ttp80) REVERT: B 53 ASP cc_start: 0.7777 (p0) cc_final: 0.7007 (p0) REVERT: B 59 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 63 ASN cc_start: 0.8154 (t0) cc_final: 0.7866 (m-40) REVERT: D 44 ARG cc_start: 0.7536 (mmp80) cc_final: 0.7055 (ttp80) REVERT: D 59 LEU cc_start: 0.8485 (tp) cc_final: 0.8284 (tt) REVERT: E 1 MET cc_start: 0.5661 (tmm) cc_final: 0.5230 (tmm) REVERT: E 163 MET cc_start: 0.7758 (mmm) cc_final: 0.7236 (mmm) REVERT: E 182 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7550 (m) REVERT: E 190 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7913 (tp30) REVERT: E 288 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7450 (tm130) REVERT: E 312 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.6723 (mtt-85) REVERT: E 317 ARG cc_start: 0.7354 (ptt90) cc_final: 0.6316 (mtm110) outliers start: 34 outliers final: 23 residues processed: 160 average time/residue: 0.0994 time to fit residues: 21.4105 Evaluate side-chains 153 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 336 MET 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: 40.0000 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.189906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.147778 restraints weight = 13904.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147732 restraints weight = 7736.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149496 restraints weight = 5779.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149732 restraints weight = 5281.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149973 restraints weight = 4809.990| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4121 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= 0.141 Angle : 0.652 8.283 11143 Z= 0.344 Chirality : 0.041 0.204 1268 Planarity : 0.005 0.050 1329 Dihedral : 19.130 130.366 1432 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.58 % Allowed : 18.32 % Favored : 77.09 % 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: -0.38 (0.28), residues: 879 helix: 0.98 (0.25), residues: 464 sheet: -1.98 (0.61), residues: 56 loop : -1.61 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 38 TYR 0.015 0.001 TYR C 74 PHE 0.025 0.002 PHE C 71 TRP 0.008 0.001 TRP F 279 HIS 0.003 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8093) covalent geometry : angle 0.65211 / 0.34 (11143) hydrogen bonds : bond 0.04423 / 4.61 ( 356) hydrogen bonds : angle 4.47536 / 6.25 ( 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 172 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8043 (t0) cc_final: 0.7453 (t70) REVERT: B 53 ASP cc_start: 0.7846 (p0) cc_final: 0.7040 (p0) REVERT: B 59 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7161 (mm) REVERT: B 63 ASN cc_start: 0.8223 (t0) cc_final: 0.7917 (m-40) REVERT: D 44 ARG cc_start: 0.7374 (mmp80) cc_final: 0.6891 (ttp80) REVERT: E 1 MET cc_start: 0.5599 (tmm) cc_final: 0.5064 (tmm) REVERT: E 6 GLN cc_start: 0.7058 (mt0) cc_final: 0.6301 (mp10) REVERT: E 190 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7994 (tp30) REVERT: E 288 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7416 (tm130) REVERT: E 317 ARG cc_start: 0.7523 (ptt90) cc_final: 0.6835 (tmm-80) REVERT: F 189 SER cc_start: 0.7597 (t) cc_final: 0.7371 (p) outliers start: 35 outliers final: 25 residues processed: 160 average time/residue: 0.0915 time to fit residues: 19.9647 Evaluate side-chains 152 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 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 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 336 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 30.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 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 = 0.4465 r_free = 0.4465 target = 0.189376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.142183 restraints weight = 13810.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146133 restraints weight = 7661.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148713 restraints weight = 5374.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.150266 restraints weight = 4388.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.150911 restraints weight = 3919.708| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4439 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= 0.142 Angle : 0.659 7.608 11143 Z= 0.349 Chirality : 0.042 0.199 1268 Planarity : 0.005 0.050 1329 Dihedral : 19.081 126.924 1432 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.19 % Allowed : 19.24 % 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: -0.32 (0.28), residues: 879 helix: 1.02 (0.25), residues: 465 sheet: -1.79 (0.62), residues: 56 loop : -1.60 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 113 TYR 0.019 0.002 TYR E 324 PHE 0.015 0.002 PHE C 71 TRP 0.009 0.002 TRP E 279 HIS 0.004 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 8093) covalent geometry : angle 0.65852 / 0.35 (11143) hydrogen bonds : bond 0.04342 / 4.52 ( 356) hydrogen bonds : angle 4.43682 / 6.17 ( 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 172 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 SER cc_start: 0.9060 (m) cc_final: 0.8826 (t) REVERT: A 28 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7361 (p) REVERT: A 81 ASP cc_start: 0.8151 (t0) cc_final: 0.7422 (t70) REVERT: A 82 SER cc_start: 0.8358 (p) cc_final: 0.7812 (t) REVERT: B 53 ASP cc_start: 0.7876 (p0) cc_final: 0.7313 (p0) REVERT: B 59 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7062 (mm) REVERT: B 63 ASN cc_start: 0.8277 (t0) cc_final: 0.7963 (m-40) REVERT: D 44 ARG cc_start: 0.7303 (mmp80) cc_final: 0.6753 (ttp80) REVERT: E 190 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8001 (tp30) REVERT: E 288 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7385 (tm130) REVERT: E 317 ARG cc_start: 0.7514 (ptt90) cc_final: 0.6956 (tmm-80) REVERT: F 311 GLN cc_start: 0.7724 (mp10) cc_final: 0.7433 (mm-40) outliers start: 32 outliers final: 24 residues processed: 160 average time/residue: 0.0985 time to fit residues: 21.1469 Evaluate side-chains 147 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 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 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 54 GLU 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 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 336 MET Chi-restraints excluded: chain F residue 3 THR 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: 3.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.4451 r_free = 0.4451 target = 0.187802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140715 restraints weight = 13906.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144822 restraints weight = 7742.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.147350 restraints weight = 5475.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148515 restraints weight = 4498.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149574 restraints weight = 4069.549| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8093 Z= 0.151 Angle : 0.687 9.393 11143 Z= 0.356 Chirality : 0.042 0.196 1268 Planarity : 0.005 0.049 1329 Dihedral : 19.082 125.664 1432 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.80 % Allowed : 20.29 % Favored : 75.92 % 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: -0.25 (0.28), residues: 879 helix: 1.11 (0.25), residues: 466 sheet: -1.68 (0.57), residues: 66 loop : -1.63 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 113 TYR 0.019 0.002 TYR E 324 PHE 0.013 0.002 PHE B 36 TRP 0.018 0.002 TRP E 279 HIS 0.005 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8093) covalent geometry : angle 0.68680 / 0.36 (11143) hydrogen bonds : bond 0.04377 / 4.60 ( 356) hydrogen bonds : angle 4.39473 / 6.06 ( 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 161 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 SER cc_start: 0.9051 (m) cc_final: 0.8659 (t) REVERT: A 28 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 44 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7712 (ptp90) REVERT: A 81 ASP cc_start: 0.8177 (t0) cc_final: 0.7472 (t70) REVERT: A 82 SER cc_start: 0.8279 (p) cc_final: 0.7777 (t) REVERT: B 59 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7059 (mm) REVERT: B 63 ASN cc_start: 0.8227 (t0) cc_final: 0.7917 (m-40) REVERT: D 44 ARG cc_start: 0.7295 (mmp80) cc_final: 0.6790 (ttp80) REVERT: E 1 MET cc_start: 0.5731 (tmm) cc_final: 0.4984 (tmm) REVERT: E 167 MET cc_start: 0.4136 (OUTLIER) cc_final: 0.3608 (tmm) REVERT: E 190 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8019 (tp30) REVERT: E 288 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7447 (tm130) REVERT: E 297 TYR cc_start: 0.8692 (m-10) cc_final: 0.8466 (m-80) REVERT: E 317 ARG cc_start: 0.7546 (ptt90) cc_final: 0.6968 (tmm-80) REVERT: F 311 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: F 326 GLN cc_start: 0.5338 (pm20) cc_final: 0.3930 (pt0) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.1034 time to fit residues: 20.5016 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 : 0.291 ------------------------------------------------------------------------------- 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 55 THR 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 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 336 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 29 optimal weight: 0.0060 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 chunk 65 optimal weight: 8.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 6 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 = 0.4480 r_free = 0.4480 target = 0.190632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.148297 restraints weight = 14011.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148453 restraints weight = 8159.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.150413 restraints weight = 5899.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.150663 restraints weight = 5384.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.151050 restraints weight = 5065.220| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8093 Z= 0.126 Angle : 0.674 9.447 11143 Z= 0.350 Chirality : 0.041 0.198 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.980 123.131 1430 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.27 % Allowed : 20.94 % Favored : 75.79 % 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: -0.14 (0.28), residues: 879 helix: 1.32 (0.25), residues: 461 sheet: -1.65 (0.57), residues: 66 loop : -1.73 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 38 TYR 0.015 0.001 TYR E 324 PHE 0.015 0.002 PHE B 36 TRP 0.012 0.002 TRP E 279 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8093) covalent geometry : angle 0.67392 / 0.35 (11143) hydrogen bonds : bond 0.03842 / 4.04 ( 356) hydrogen bonds : angle 4.24545 / 5.82 ( 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 164 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7442 (tp30) cc_final: 0.7171 (tp30) REVERT: A 23 SER cc_start: 0.8996 (m) cc_final: 0.8753 (t) REVERT: A 44 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7686 (ptp90) REVERT: A 81 ASP cc_start: 0.8029 (t0) cc_final: 0.7432 (t70) REVERT: A 82 SER cc_start: 0.8134 (p) cc_final: 0.7626 (t) REVERT: B 53 ASP cc_start: 0.8041 (p0) cc_final: 0.7108 (p0) REVERT: B 59 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7007 (mm) REVERT: B 63 ASN cc_start: 0.8110 (t0) cc_final: 0.7846 (m-40) REVERT: C 85 TYR cc_start: 0.6926 (t80) cc_final: 0.6450 (t80) REVERT: D 44 ARG cc_start: 0.7162 (mmp80) cc_final: 0.6697 (ttp80) REVERT: E 163 MET cc_start: 0.7081 (mpp) cc_final: 0.6860 (mpp) REVERT: E 167 MET cc_start: 0.4040 (OUTLIER) cc_final: 0.3484 (mmm) REVERT: E 190 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7990 (tp30) REVERT: E 288 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7337 (tm130) REVERT: E 317 ARG cc_start: 0.7547 (ptt90) cc_final: 0.7117 (tmm-80) REVERT: F 311 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7435 (mm-40) REVERT: F 330 PHE cc_start: 0.6750 (p90) cc_final: 0.6230 (p90) outliers start: 25 outliers final: 17 residues processed: 155 average time/residue: 0.0987 time to fit residues: 20.2561 Evaluate side-chains 146 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 292 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 336 MET 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: 9.9990 chunk 53 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 83 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.188928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.142841 restraints weight = 13910.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146721 restraints weight = 7797.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149136 restraints weight = 5559.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150438 restraints weight = 4580.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151409 restraints weight = 4124.960| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8093 Z= 0.136 Angle : 0.683 9.444 11143 Z= 0.353 Chirality : 0.041 0.193 1268 Planarity : 0.005 0.049 1329 Dihedral : 19.009 122.338 1428 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.01 % Allowed : 21.34 % Favored : 75.65 % 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: -0.09 (0.28), residues: 879 helix: 1.37 (0.25), residues: 461 sheet: -1.53 (0.57), residues: 66 loop : -1.76 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.027 0.001 TYR F 229 PHE 0.019 0.002 PHE E 164 TRP 0.012 0.002 TRP E 279 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8093) covalent geometry : angle 0.68290 / 0.35 (11143) hydrogen bonds : bond 0.03932 / 4.18 ( 356) hydrogen bonds : angle 4.24084 / 5.79 ( 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 161 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7356 (tp30) cc_final: 0.7070 (tp30) REVERT: A 23 SER cc_start: 0.9053 (m) cc_final: 0.8663 (t) REVERT: A 80 ARG cc_start: 0.7456 (tpp-160) cc_final: 0.7038 (tpt-90) REVERT: A 81 ASP cc_start: 0.8130 (t0) cc_final: 0.7493 (t70) REVERT: A 82 SER cc_start: 0.8158 (p) cc_final: 0.7643 (t) REVERT: B 59 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7039 (mm) REVERT: B 60 ASN cc_start: 0.8214 (t0) cc_final: 0.7821 (t0) REVERT: B 63 ASN cc_start: 0.8073 (t0) cc_final: 0.7816 (m-40) REVERT: C 85 TYR cc_start: 0.6716 (t80) cc_final: 0.6334 (t80) REVERT: D 44 ARG cc_start: 0.7217 (mmp80) cc_final: 0.6680 (ttp80) REVERT: E 167 MET cc_start: 0.3887 (OUTLIER) cc_final: 0.3306 (mmm) REVERT: E 190 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7882 (tp30) REVERT: E 233 ASP cc_start: 0.7824 (p0) cc_final: 0.7506 (p0) REVERT: E 288 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7320 (tm130) REVERT: E 317 ARG cc_start: 0.7541 (ptt90) cc_final: 0.7079 (tmm-80) REVERT: F 311 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7447 (mm-40) REVERT: F 326 GLN cc_start: 0.5410 (pm20) cc_final: 0.4133 (pt0) REVERT: F 330 PHE cc_start: 0.6806 (p90) cc_final: 0.6297 (p90) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.0992 time to fit residues: 20.3673 Evaluate side-chains 149 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 LEU 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 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 292 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 336 MET 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: 5.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.188358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144765 restraints weight = 13874.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.145268 restraints weight = 8427.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146258 restraints weight = 6028.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146834 restraints weight = 5478.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.147134 restraints weight = 5133.222| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8093 Z= 0.142 Angle : 0.692 9.632 11143 Z= 0.358 Chirality : 0.041 0.192 1268 Planarity : 0.005 0.049 1329 Dihedral : 19.057 122.208 1427 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.01 % Allowed : 21.86 % Favored : 75.13 % 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: -0.07 (0.28), residues: 879 helix: 1.40 (0.25), residues: 458 sheet: -1.47 (0.58), residues: 66 loop : -1.75 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 38 TYR 0.019 0.001 TYR F 229 PHE 0.014 0.002 PHE F 4 TRP 0.013 0.002 TRP E 279 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8093) covalent geometry : angle 0.69223 / 0.36 (11143) hydrogen bonds : bond 0.04073 / 4.31 ( 356) hydrogen bonds : angle 4.24920 / 5.79 ( 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 158 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7746 (tp30) cc_final: 0.7485 (tp30) REVERT: A 23 SER cc_start: 0.9146 (m) cc_final: 0.8741 (t) REVERT: A 81 ASP cc_start: 0.8283 (t0) cc_final: 0.7643 (t70) REVERT: B 59 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7085 (mm) REVERT: B 60 ASN cc_start: 0.8393 (t0) cc_final: 0.7868 (t0) REVERT: B 63 ASN cc_start: 0.8280 (t0) cc_final: 0.7990 (m-40) REVERT: C 85 TYR cc_start: 0.7090 (t80) cc_final: 0.6615 (t80) REVERT: D 44 ARG cc_start: 0.7218 (mmp80) cc_final: 0.6624 (ttp80) REVERT: E 167 MET cc_start: 0.4178 (OUTLIER) cc_final: 0.3624 (mmm) REVERT: E 190 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7835 (tp30) REVERT: E 286 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6890 (m) REVERT: E 288 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7183 (tm130) REVERT: E 317 ARG cc_start: 0.7537 (ptt90) cc_final: 0.7121 (tmm-80) REVERT: F 311 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: F 326 GLN cc_start: 0.5377 (pm20) cc_final: 0.4186 (pt0) REVERT: F 330 PHE cc_start: 0.6812 (p90) cc_final: 0.6256 (p90) outliers start: 23 outliers final: 17 residues processed: 149 average time/residue: 0.0761 time to fit residues: 15.4363 Evaluate side-chains 156 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 292 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 339 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 0.0010 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.189180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.142606 restraints weight = 13872.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.146637 restraints weight = 7694.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149166 restraints weight = 5422.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150481 restraints weight = 4445.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.151359 restraints weight = 3998.018| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8093 Z= 0.132 Angle : 0.703 9.441 11143 Z= 0.362 Chirality : 0.043 0.397 1268 Planarity : 0.005 0.049 1329 Dihedral : 19.038 121.778 1427 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.62 % Allowed : 22.64 % Favored : 74.74 % 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: -0.10 (0.28), residues: 879 helix: 1.40 (0.25), residues: 461 sheet: -1.57 (0.57), residues: 65 loop : -1.81 (0.27), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 38 TYR 0.023 0.001 TYR F 229 PHE 0.016 0.002 PHE F 4 TRP 0.012 0.002 TRP E 279 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8093) covalent geometry : angle 0.70326 / 0.36 (11143) hydrogen bonds : bond 0.03940 / 4.18 ( 356) hydrogen bonds : angle 4.20554 / 5.72 ( 1018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.91 seconds wall clock time: 26 minutes 23.33 seconds (1583.33 seconds total)