Starting phenix.real_space_refine on Sat May 2 17:42:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uer_64090/05_2026/9uer_64090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uer_64090/05_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_64090/05_2026/9uer_64090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uer_64090/05_2026/9uer_64090.map" model { file = "/net/cci-nas-00/data/ceres_data/9uer_64090/05_2026/9uer_64090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uer_64090/05_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-2.1rc2-6044/lib/python3.9/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: 1.93, per 1000 atoms: 0.25 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: 0.59 Conformation dependent library (CDL) restraints added in 376.6 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: 0.73 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: 0.85 Time building geometry restraints manager: 0.78 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=" 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=" CA SER A 10 " pdb=" CB SER A 10 " ideal model delta sigma weight residual 1.533 1.490 0.043 1.51e-02 4.39e+03 8.23e+00 bond pdb=" N SER D 10 " pdb=" CA SER D 10 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.31e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.40e-02 5.10e+03 5.77e+00 bond pdb=" N GLN F 288 " pdb=" CA GLN F 288 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.45e-02 4.76e+03 5.66e+00 ... (remaining 8088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10403 1.62 - 3.24: 592 3.24 - 4.86: 110 4.86 - 6.48: 26 6.48 - 8.10: 12 Bond angle restraints: 11143 Sorted by residual: 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=" C GLN F 305 " pdb=" N LEU F 306 " pdb=" CA LEU F 306 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " pdb=" CG ASP A 81 " ideal model delta sigma weight residual 112.60 116.70 -4.10 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N LYS E 45 " pdb=" CA LYS E 45 " pdb=" C LYS E 45 " ideal model delta sigma weight residual 111.14 107.08 4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" C3' DC G 11 " pdb=" O3' DC G 11 " pdb=" P DT G 12 " ideal model delta sigma weight residual 120.20 114.58 5.62 1.50e+00 4.44e-01 1.40e+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 - 0.103: 1206 0.103 - 0.206: 53 0.206 - 0.309: 2 0.309 - 0.412: 0 0.412 - 0.515: 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 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.64e+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 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.63e+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 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.48e+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: 0.380 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 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 : 0.006 0.061 8093 Z= 0.307 Angle : 0.885 8.096 11143 Z= 0.511 Chirality : 0.060 0.515 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 covalent geometry : bond 0.00647 ( 8093) covalent geometry : angle 0.88469 (11143) hydrogen bonds : bond 0.16483 ( 356) hydrogen bonds : angle 7.38863 ( 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 : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6955 (mm110) REVERT: D 100 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: E 6 GLN cc_start: 0.6749 (mt0) cc_final: 0.6376 (mp10) REVERT: E 263 SER cc_start: 0.8178 (p) cc_final: 0.7387 (p) REVERT: E 279 TRP cc_start: 0.5638 (t60) cc_final: 0.5422 (t60) REVERT: E 312 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.7024 (mtt180) REVERT: E 317 ARG cc_start: 0.7062 (ptt90) cc_final: 0.6805 (ptt90) REVERT: E 342 MET cc_start: 0.5502 (ttt) cc_final: 0.5024 (ttt) REVERT: F 311 GLN cc_start: 0.7125 (mp10) cc_final: 0.6901 (mp-120) outliers start: 80 outliers final: 25 residues processed: 280 average time/residue: 0.1025 time to fit residues: 36.5712 Evaluate side-chains 160 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 33 ASN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 34 ASN D 60 ASN E 332 HIS F 42 GLN F 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.190960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.147303 restraints weight = 13853.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.148006 restraints weight = 8252.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150280 restraints weight = 5705.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.150497 restraints weight = 4982.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.150697 restraints weight = 4636.380| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8093 Z= 0.184 Angle : 0.713 8.444 11143 Z= 0.377 Chirality : 0.042 0.152 1268 Planarity : 0.006 0.050 1329 Dihedral : 19.163 132.465 1471 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 3.93 % Allowed : 14.92 % Favored : 81.15 % 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: -0.79 (0.27), residues: 879 helix: 0.46 (0.23), residues: 470 sheet: -2.11 (0.64), residues: 56 loop : -1.55 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 253 TYR 0.023 0.002 TYR E 324 PHE 0.017 0.002 PHE A 71 TRP 0.014 0.002 TRP F 279 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8093) covalent geometry : angle 0.71332 (11143) hydrogen bonds : bond 0.04935 ( 356) hydrogen bonds : angle 4.70568 ( 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 177 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7795 (t0) cc_final: 0.7537 (t70) REVERT: A 82 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7455 (t) REVERT: B 44 ARG cc_start: 0.8350 (tmm-80) cc_final: 0.8018 (ttp80) REVERT: C 99 CYS cc_start: 0.7866 (m) cc_final: 0.7595 (m) REVERT: D 59 LEU cc_start: 0.8452 (tp) cc_final: 0.8238 (tt) REVERT: E 161 ILE cc_start: 0.7735 (tp) cc_final: 0.7508 (tt) REVERT: E 190 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7949 (tp30) REVERT: E 288 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7097 (tm130) REVERT: E 297 TYR cc_start: 0.8665 (m-10) cc_final: 0.8444 (m-10) REVERT: F 312 ARG cc_start: 0.7042 (tpp-160) cc_final: 0.6207 (tpm170) outliers start: 30 outliers final: 19 residues processed: 169 average time/residue: 0.0812 time to fit residues: 18.6792 Evaluate side-chains 148 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 SER 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 61 VAL Chi-restraints excluded: chain C residue 66 VAL 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 40 SER Chi-restraints excluded: chain E residue 288 GLN 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 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 HIS E 332 HIS ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.190302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143285 restraints weight = 13876.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147382 restraints weight = 7627.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149936 restraints weight = 5358.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151431 restraints weight = 4409.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.152092 restraints weight = 3957.893| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8093 Z= 0.142 Angle : 0.645 8.251 11143 Z= 0.334 Chirality : 0.040 0.161 1268 Planarity : 0.005 0.050 1329 Dihedral : 18.818 123.866 1436 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.88 % Allowed : 18.32 % Favored : 78.80 % 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: -0.30 (0.27), residues: 879 helix: 0.99 (0.24), residues: 466 sheet: -1.72 (0.59), residues: 66 loop : -1.52 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 253 TYR 0.014 0.001 TYR E 324 PHE 0.015 0.002 PHE B 36 TRP 0.012 0.002 TRP E 279 HIS 0.015 0.002 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8093) covalent geometry : angle 0.64483 (11143) hydrogen bonds : bond 0.04024 ( 356) hydrogen bonds : angle 4.31632 ( 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 173 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8035 (t0) cc_final: 0.7584 (t70) REVERT: B 53 ASP cc_start: 0.7889 (p0) cc_final: 0.7080 (p0) REVERT: B 59 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7177 (mm) REVERT: B 63 ASN cc_start: 0.8238 (t0) cc_final: 0.7920 (m-40) REVERT: C 112 GLU cc_start: 0.7300 (tp30) cc_final: 0.6861 (tp30) REVERT: D 44 ARG cc_start: 0.7291 (mmp80) cc_final: 0.6722 (ttp80) REVERT: E 160 ASP cc_start: 0.8645 (m-30) cc_final: 0.8340 (m-30) REVERT: E 161 ILE cc_start: 0.7761 (tp) cc_final: 0.7530 (tt) REVERT: E 163 MET cc_start: 0.7363 (tpp) cc_final: 0.6854 (mpp) REVERT: E 233 ASP cc_start: 0.7816 (p0) cc_final: 0.7528 (p0) REVERT: E 317 ARG cc_start: 0.7097 (ptt90) cc_final: 0.6797 (tmm-80) REVERT: F 189 SER cc_start: 0.7612 (t) cc_final: 0.7344 (p) REVERT: F 312 ARG cc_start: 0.7163 (tpp-160) cc_final: 0.6569 (tpm170) REVERT: F 319 ASN cc_start: 0.7868 (m110) cc_final: 0.7092 (t0) outliers start: 22 outliers final: 12 residues processed: 165 average time/residue: 0.0976 time to fit residues: 21.1570 Evaluate side-chains 142 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 ILE 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 D residue 95 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 336 MET 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: 0.0020 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.184329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.139247 restraints weight = 14048.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139721 restraints weight = 8642.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.141610 restraints weight = 6263.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.142380 restraints weight = 5185.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.142576 restraints weight = 4934.701| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8093 Z= 0.202 Angle : 0.691 9.708 11143 Z= 0.362 Chirality : 0.042 0.156 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.976 129.552 1429 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.19 % Allowed : 17.93 % Favored : 77.88 % 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: -0.44 (0.27), residues: 879 helix: 0.93 (0.24), residues: 461 sheet: -1.63 (0.66), residues: 57 loop : -1.69 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 113 TYR 0.026 0.002 TYR E 324 PHE 0.018 0.002 PHE B 11 TRP 0.010 0.002 TRP E 279 HIS 0.019 0.002 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8093) covalent geometry : angle 0.69056 (11143) hydrogen bonds : bond 0.04901 ( 356) hydrogen bonds : angle 4.43307 ( 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 178 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7755 (p) REVERT: A 79 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7746 (mp) REVERT: A 81 ASP cc_start: 0.8204 (t0) cc_final: 0.7814 (t70) REVERT: B 59 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7440 (mm) REVERT: B 60 ASN cc_start: 0.8721 (t0) cc_final: 0.7931 (t0) REVERT: B 63 ASN cc_start: 0.8263 (t0) cc_final: 0.7995 (m-40) REVERT: C 84 ASP cc_start: 0.7548 (p0) cc_final: 0.7158 (p0) REVERT: D 44 ARG cc_start: 0.7564 (mmp80) cc_final: 0.7021 (ttp80) REVERT: D 68 GLU cc_start: 0.8014 (mp0) cc_final: 0.7776 (mp0) REVERT: E 1 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.5121 (ppp) REVERT: E 161 ILE cc_start: 0.7876 (tp) cc_final: 0.7635 (tt) REVERT: E 233 ASP cc_start: 0.7852 (p0) cc_final: 0.7457 (p0) REVERT: E 317 ARG cc_start: 0.7246 (ptt90) cc_final: 0.6734 (tmm-80) REVERT: E 318 GLU cc_start: 0.8572 (pt0) cc_final: 0.8316 (pt0) REVERT: F 312 ARG cc_start: 0.7360 (tpp-160) cc_final: 0.6882 (tpm170) REVERT: F 331 GLN cc_start: 0.5753 (pm20) cc_final: 0.4765 (mm-40) outliers start: 32 outliers final: 19 residues processed: 167 average time/residue: 0.0850 time to fit residues: 19.1996 Evaluate side-chains 150 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 VAL 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 66 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 186 PHE 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 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.182900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138742 restraints weight = 13958.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.138458 restraints weight = 9194.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139528 restraints weight = 6877.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140190 restraints weight = 6421.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140183 restraints weight = 5892.269| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8093 Z= 0.204 Angle : 0.693 9.171 11143 Z= 0.361 Chirality : 0.042 0.202 1268 Planarity : 0.005 0.051 1329 Dihedral : 18.921 129.240 1429 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.71 % Allowed : 18.59 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.27), residues: 879 helix: 0.83 (0.24), residues: 464 sheet: -1.54 (0.61), residues: 67 loop : -1.76 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 49 TYR 0.043 0.002 TYR E 324 PHE 0.015 0.002 PHE B 11 TRP 0.008 0.002 TRP F 279 HIS 0.010 0.002 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8093) covalent geometry : angle 0.69297 (11143) hydrogen bonds : bond 0.04803 ( 356) hydrogen bonds : angle 4.42681 ( 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 175 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 81 ASP cc_start: 0.8155 (t0) cc_final: 0.7800 (t70) REVERT: B 53 ASP cc_start: 0.7992 (p0) cc_final: 0.7049 (p0) REVERT: B 59 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7476 (mm) REVERT: B 60 ASN cc_start: 0.8730 (t0) cc_final: 0.7910 (t0) REVERT: B 63 ASN cc_start: 0.8170 (t0) cc_final: 0.7912 (m-40) REVERT: D 44 ARG cc_start: 0.7468 (mmp80) cc_final: 0.7015 (ttp80) REVERT: D 68 GLU cc_start: 0.7963 (mp0) cc_final: 0.7707 (mp0) REVERT: E 1 MET cc_start: 0.5351 (OUTLIER) cc_final: 0.4928 (ppp) REVERT: E 163 MET cc_start: 0.7593 (mpp) cc_final: 0.6995 (mpp) REVERT: E 233 ASP cc_start: 0.7865 (p0) cc_final: 0.7456 (p0) REVERT: E 317 ARG cc_start: 0.7321 (ptt90) cc_final: 0.7108 (ptt90) REVERT: F 189 SER cc_start: 0.7687 (t) cc_final: 0.7450 (p) REVERT: F 311 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7149 (mm-40) REVERT: F 312 ARG cc_start: 0.7550 (tpp-160) cc_final: 0.7036 (tpm170) REVERT: F 331 GLN cc_start: 0.5737 (pm20) cc_final: 0.4817 (tp-100) outliers start: 36 outliers final: 22 residues processed: 163 average time/residue: 0.0901 time to fit residues: 19.5831 Evaluate side-chains 151 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 66 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 61 VAL 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 55 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 186 PHE 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 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.0570 chunk 22 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.0040 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 chunk 74 optimal weight: 20.0000 overall best weight: 0.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN D 100 GLN E 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.189004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.142464 restraints weight = 13764.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146460 restraints weight = 7711.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.149022 restraints weight = 5473.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.150283 restraints weight = 4527.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151233 restraints weight = 4102.072| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8093 Z= 0.123 Angle : 0.630 8.626 11143 Z= 0.322 Chirality : 0.038 0.174 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.625 123.736 1429 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.53 % Allowed : 20.55 % 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: -0.10 (0.28), residues: 879 helix: 1.27 (0.24), residues: 473 sheet: -1.08 (0.62), residues: 67 loop : -1.82 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 38 TYR 0.023 0.001 TYR E 324 PHE 0.015 0.001 PHE B 36 TRP 0.008 0.001 TRP F 279 HIS 0.017 0.001 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8093) covalent geometry : angle 0.63039 (11143) hydrogen bonds : bond 0.03409 ( 356) hydrogen bonds : angle 4.04042 ( 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 176 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7406 (p0) cc_final: 0.7020 (p0) REVERT: A 81 ASP cc_start: 0.8130 (t0) cc_final: 0.7788 (t70) REVERT: B 53 ASP cc_start: 0.7687 (p0) cc_final: 0.6898 (p0) REVERT: B 59 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6982 (mm) REVERT: B 60 ASN cc_start: 0.8349 (t0) cc_final: 0.7777 (t0) REVERT: B 63 ASN cc_start: 0.8088 (t0) cc_final: 0.7843 (m-40) REVERT: D 44 ARG cc_start: 0.6858 (mmp80) cc_final: 0.6344 (ttp80) REVERT: D 60 ASN cc_start: 0.8284 (m110) cc_final: 0.7925 (m110) REVERT: E 163 MET cc_start: 0.7391 (tpp) cc_final: 0.6768 (mpp) REVERT: E 233 ASP cc_start: 0.7849 (p0) cc_final: 0.7578 (p0) REVERT: E 286 THR cc_start: 0.6294 (OUTLIER) cc_final: 0.5953 (m) REVERT: F 311 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7148 (mm-40) REVERT: F 312 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7034 (tpm170) outliers start: 27 outliers final: 14 residues processed: 167 average time/residue: 0.1004 time to fit residues: 21.7889 Evaluate side-chains 149 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS Chi-restraints excluded: chain E residue 336 MET 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: 2.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 37 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.189667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.142931 restraints weight = 13858.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.146959 restraints weight = 7827.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149457 restraints weight = 5566.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150588 restraints weight = 4591.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151659 restraints weight = 4165.522| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8093 Z= 0.124 Angle : 0.646 8.220 11143 Z= 0.329 Chirality : 0.038 0.171 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.606 125.696 1426 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.62 % Allowed : 21.99 % Favored : 75.39 % 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: 0.03 (0.28), residues: 879 helix: 1.36 (0.24), residues: 475 sheet: -0.98 (0.59), residues: 67 loop : -1.77 (0.28), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 49 TYR 0.024 0.001 TYR F 229 PHE 0.019 0.002 PHE F 186 TRP 0.006 0.001 TRP E 279 HIS 0.018 0.001 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8093) covalent geometry : angle 0.64572 (11143) hydrogen bonds : bond 0.03400 ( 356) hydrogen bonds : angle 4.02808 ( 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 157 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7465 (p0) cc_final: 0.7137 (p0) REVERT: A 81 ASP cc_start: 0.8186 (t0) cc_final: 0.7909 (t70) REVERT: B 53 ASP cc_start: 0.7715 (p0) cc_final: 0.6978 (p0) REVERT: B 59 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7251 (mm) REVERT: B 60 ASN cc_start: 0.8193 (t0) cc_final: 0.7834 (t0) REVERT: B 63 ASN cc_start: 0.8072 (t0) cc_final: 0.7810 (m-40) REVERT: D 44 ARG cc_start: 0.6804 (mmp80) cc_final: 0.6247 (ttp80) REVERT: D 60 ASN cc_start: 0.8203 (m110) cc_final: 0.7835 (m110) REVERT: E 233 ASP cc_start: 0.7824 (p0) cc_final: 0.7525 (p0) REVERT: E 286 THR cc_start: 0.6190 (OUTLIER) cc_final: 0.5846 (m) REVERT: F 311 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7228 (mm-40) REVERT: F 312 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7155 (tpm170) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.0876 time to fit residues: 17.3480 Evaluate side-chains 143 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 67 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 E residue 37 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN E 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.189239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142655 restraints weight = 13825.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.146483 restraints weight = 7933.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.148926 restraints weight = 5697.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150367 restraints weight = 4713.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.150836 restraints weight = 4235.153| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8093 Z= 0.131 Angle : 0.664 12.418 11143 Z= 0.335 Chirality : 0.039 0.166 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.594 128.942 1426 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 23.30 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.28), residues: 879 helix: 1.42 (0.24), residues: 470 sheet: -0.82 (0.59), residues: 65 loop : -1.74 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.023 0.001 TYR E 324 PHE 0.019 0.002 PHE C 71 TRP 0.006 0.001 TRP F 48 HIS 0.004 0.001 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8093) covalent geometry : angle 0.66355 (11143) hydrogen bonds : bond 0.03578 ( 356) hydrogen bonds : angle 4.06342 ( 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 144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7787 (tpt170) cc_final: 0.7574 (tpt170) REVERT: A 81 ASP cc_start: 0.8150 (t0) cc_final: 0.7900 (t70) REVERT: B 53 ASP cc_start: 0.7663 (p0) cc_final: 0.6934 (p0) REVERT: B 59 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7322 (mm) REVERT: B 60 ASN cc_start: 0.8207 (t0) cc_final: 0.7877 (t0) REVERT: B 63 ASN cc_start: 0.8002 (t0) cc_final: 0.7759 (m-40) REVERT: D 44 ARG cc_start: 0.6899 (mmp80) cc_final: 0.6333 (ttp80) REVERT: D 60 ASN cc_start: 0.8226 (m110) cc_final: 0.7859 (m110) REVERT: E 1 MET cc_start: 0.4528 (ppp) cc_final: 0.4313 (ppp) REVERT: E 233 ASP cc_start: 0.7849 (p0) cc_final: 0.7523 (p0) REVERT: E 286 THR cc_start: 0.6338 (OUTLIER) cc_final: 0.5971 (m) REVERT: F 1 MET cc_start: 0.6276 (pmm) cc_final: 0.4379 (mmt) REVERT: F 311 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7289 (mm-40) REVERT: F 312 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7388 (tpm170) outliers start: 19 outliers final: 14 residues processed: 136 average time/residue: 0.0897 time to fit residues: 16.3394 Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 59 LEU 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 E residue 37 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN E 42 GLN E 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.188803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141943 restraints weight = 13758.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.145770 restraints weight = 7969.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148147 restraints weight = 5777.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149519 restraints weight = 4807.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.150127 restraints weight = 4340.941| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8093 Z= 0.133 Angle : 0.658 9.781 11143 Z= 0.336 Chirality : 0.039 0.217 1268 Planarity : 0.005 0.050 1329 Dihedral : 18.601 130.841 1425 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.75 % Allowed : 23.17 % Favored : 74.08 % 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: 1.39 (0.25), residues: 473 sheet: -0.87 (0.59), residues: 65 loop : -1.74 (0.28), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.024 0.001 TYR E 324 PHE 0.014 0.002 PHE B 36 TRP 0.007 0.001 TRP F 279 HIS 0.010 0.001 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8093) covalent geometry : angle 0.65777 (11143) hydrogen bonds : bond 0.03629 ( 356) hydrogen bonds : angle 4.06378 ( 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 148 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7471 (p) REVERT: A 51 ASP cc_start: 0.7345 (p0) cc_final: 0.7091 (p0) REVERT: A 80 ARG cc_start: 0.7792 (tpt170) cc_final: 0.7568 (tpt170) REVERT: A 81 ASP cc_start: 0.8203 (t0) cc_final: 0.7964 (t70) REVERT: B 53 ASP cc_start: 0.7623 (p0) cc_final: 0.6924 (p0) REVERT: B 59 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7362 (mm) REVERT: B 60 ASN cc_start: 0.8209 (t0) cc_final: 0.7894 (t0) REVERT: B 63 ASN cc_start: 0.8014 (t0) cc_final: 0.7777 (m-40) REVERT: D 44 ARG cc_start: 0.7003 (mmp80) cc_final: 0.6453 (ttp80) REVERT: D 60 ASN cc_start: 0.8208 (m110) cc_final: 0.7854 (m110) REVERT: E 1 MET cc_start: 0.4541 (ppp) cc_final: 0.4240 (ppp) REVERT: E 233 ASP cc_start: 0.7882 (p0) cc_final: 0.7555 (p0) REVERT: E 286 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.6157 (m) REVERT: F 1 MET cc_start: 0.6136 (pmm) cc_final: 0.4318 (mmt) REVERT: F 311 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7250 (mm-40) REVERT: F 312 ARG cc_start: 0.7638 (tpp-160) cc_final: 0.7383 (tpm170) outliers start: 21 outliers final: 15 residues processed: 140 average time/residue: 0.0936 time to fit residues: 17.2653 Evaluate side-chains 143 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 59 LEU 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 E residue 9 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.0070 chunk 69 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.187394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.140237 restraints weight = 13670.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143927 restraints weight = 8146.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146272 restraints weight = 5990.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147614 restraints weight = 5029.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148172 restraints weight = 4563.372| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8093 Z= 0.147 Angle : 0.682 8.412 11143 Z= 0.350 Chirality : 0.039 0.203 1268 Planarity : 0.005 0.050 1329 Dihedral : 18.664 132.094 1425 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.62 % Allowed : 23.30 % Favored : 74.08 % 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: 1.25 (0.25), residues: 475 sheet: -1.18 (0.59), residues: 67 loop : -1.78 (0.28), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.025 0.002 TYR E 324 PHE 0.016 0.002 PHE B 36 TRP 0.007 0.001 TRP F 279 HIS 0.015 0.002 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8093) covalent geometry : angle 0.68169 (11143) hydrogen bonds : bond 0.03825 ( 356) hydrogen bonds : angle 4.13228 ( 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 147 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7558 (p) REVERT: A 51 ASP cc_start: 0.7339 (p0) cc_final: 0.7118 (p0) REVERT: A 80 ARG cc_start: 0.7870 (tpt170) cc_final: 0.7640 (tpt170) REVERT: A 81 ASP cc_start: 0.8225 (t0) cc_final: 0.7974 (t70) REVERT: B 53 ASP cc_start: 0.7719 (p0) cc_final: 0.7050 (p0) REVERT: B 59 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7434 (mm) REVERT: B 60 ASN cc_start: 0.8314 (t0) cc_final: 0.7920 (t0) REVERT: B 63 ASN cc_start: 0.8045 (t0) cc_final: 0.7778 (m-40) REVERT: D 44 ARG cc_start: 0.7093 (mmp80) cc_final: 0.6584 (ttp80) REVERT: D 60 ASN cc_start: 0.8251 (m110) cc_final: 0.7886 (m110) REVERT: E 1 MET cc_start: 0.4511 (ppp) cc_final: 0.4185 (ppp) REVERT: E 233 ASP cc_start: 0.7898 (p0) cc_final: 0.7530 (p0) REVERT: E 286 THR cc_start: 0.6586 (OUTLIER) cc_final: 0.6234 (m) REVERT: F 1 MET cc_start: 0.6131 (pmm) cc_final: 0.4367 (mmt) REVERT: F 311 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7277 (mm-40) REVERT: F 312 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7530 (tpm170) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.0941 time to fit residues: 17.5733 Evaluate side-chains 139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 66 VAL 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 55 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.190050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143465 restraints weight = 13683.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147130 restraints weight = 8201.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149465 restraints weight = 6030.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.150823 restraints weight = 5059.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.151411 restraints weight = 4584.431| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8093 Z= 0.127 Angle : 0.662 9.167 11143 Z= 0.339 Chirality : 0.039 0.191 1268 Planarity : 0.005 0.049 1329 Dihedral : 18.610 130.672 1424 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.23 % Allowed : 23.69 % Favored : 74.08 % 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: 0.01 (0.28), residues: 879 helix: 1.31 (0.25), residues: 475 sheet: -1.24 (0.58), residues: 71 loop : -1.64 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 113 TYR 0.022 0.001 TYR E 324 PHE 0.016 0.001 PHE B 36 TRP 0.009 0.001 TRP F 279 HIS 0.011 0.001 HIS E 332 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8093) covalent geometry : angle 0.66225 (11143) hydrogen bonds : bond 0.03468 ( 356) hydrogen bonds : angle 4.03377 ( 1018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1419.10 seconds wall clock time: 25 minutes 7.46 seconds (1507.46 seconds total)