Starting phenix.real_space_refine on Fri Sep 11 08:50:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqy_20456/09_2026/6pqy_20456.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqy_20456/09_2026/6pqy_20456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pqy_20456/09_2026/6pqy_20456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqy_20456/09_2026/6pqy_20456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqy_20456/09_2026/6pqy_20456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqy_20456/09_2026/6pqy_20456.map" } resolution = 4.2 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= 0.000 sd= 0.002 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 64 5.49 5 S 34 5.16 5 C 5324 2.51 5 N 1496 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3689 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3689 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8690 At special positions: 0 Unit cell: (85.05, 122.85, 92.4, 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 34 16.00 P 64 15.00 O 1772 8.00 N 1496 7.00 C 5324 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: 0.77 Conformation dependent library (CDL) restraints added in 197.5 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 52.6% alpha, 14.8% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 4.031A pdb=" N GLY A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.582A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.722A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 106 removed outlier: 4.271A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.030A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 275 through 289 removed outlier: 3.697A pdb=" N VAL A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 removed outlier: 3.690A pdb=" N ASN A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.504A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 374 " --> pdb=" O GLN A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.571A pdb=" N HIS A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.512A pdb=" N GLU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.892A pdb=" N ASN A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.554A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 removed outlier: 4.031A pdb=" N GLY D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.582A pdb=" N GLU D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.721A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 106 removed outlier: 4.270A pdb=" N ILE D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.031A pdb=" N TYR D 174 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.698A pdb=" N VAL D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 322 removed outlier: 3.690A pdb=" N ASN D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 347 through 355 Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.505A pdb=" N ILE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 398 Processing helix chain 'D' and resid 404 through 412 removed outlier: 3.572A pdb=" N HIS D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.512A pdb=" N GLU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 448 Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.892A pdb=" N ASN D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.554A pdb=" N LEU D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 125 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 119 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 156 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 117 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU A 116 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N LEU A 218 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N LEU A 118 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N MET A 220 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 11.195A pdb=" N SER A 120 " --> pdb=" O MET A 220 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N MET A 222 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP A 122 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR D 149 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 180 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D 147 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR D 149 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 180 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D 147 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 125 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE D 119 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU D 156 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 117 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU D 116 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N LEU D 218 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N LEU D 118 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N MET D 220 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N SER D 120 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N MET D 222 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP D 122 " --> pdb=" O MET D 222 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.93 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: 2151 1.33 - 1.45: 1973 1.45 - 1.57: 4688 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 8988 Sorted by residual: bond pdb=" C3' DT C 3 " pdb=" O3' DT C 3 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.64e+01 bond pdb=" C3' DT F 3 " pdb=" O3' DT F 3 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.63e+01 bond pdb=" C3' DT C 2 " pdb=" O3' DT C 2 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" N9 DA F 7 " pdb=" C4 DA F 7 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.46e+01 bond pdb=" C3' DT F 2 " pdb=" O3' DT F 2 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 11831 2.32 - 4.63: 528 4.63 - 6.95: 29 6.95 - 9.27: 9 9.27 - 11.59: 3 Bond angle restraints: 12400 Sorted by residual: angle pdb=" O4' DC C 9 " pdb=" C4' DC C 9 " pdb=" C3' DC C 9 " ideal model delta sigma weight residual 106.00 102.70 3.30 6.00e-01 2.78e+00 3.02e+01 angle pdb=" O4' DC F 9 " pdb=" C4' DC F 9 " pdb=" C3' DC F 9 " ideal model delta sigma weight residual 106.00 102.71 3.29 6.00e-01 2.78e+00 3.01e+01 angle pdb=" N3 DT C 2 " pdb=" C4 DT C 2 " pdb=" O4 DT C 2 " ideal model delta sigma weight residual 119.90 122.79 -2.89 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O4' DA B 25 " pdb=" C4' DA B 25 " pdb=" C3' DA B 25 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" N3 DT F 2 " pdb=" C4 DT F 2 " pdb=" O4 DT F 2 " ideal model delta sigma weight residual 119.90 122.76 -2.86 6.00e-01 2.78e+00 2.27e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4952 35.87 - 71.75: 328 71.75 - 107.62: 10 107.62 - 143.49: 0 143.49 - 179.36: 10 Dihedral angle restraints: 5300 sinusoidal: 2588 harmonic: 2712 Sorted by residual: dihedral pdb=" CA ASP D 161 " pdb=" C ASP D 161 " pdb=" N THR D 162 " pdb=" CA THR D 162 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA SER A 453 " pdb=" C SER A 453 " pdb=" N ARG A 454 " pdb=" CA ARG A 454 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 5297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1189 0.087 - 0.174: 171 0.174 - 0.261: 29 0.261 - 0.348: 8 0.348 - 0.435: 3 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C3' DC F 12 " pdb=" C4' DC F 12 " pdb=" O3' DC F 12 " pdb=" C2' DC F 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.30 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" C3' DC C 12 " pdb=" C4' DC C 12 " pdb=" O3' DC C 12 " pdb=" C2' DC C 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.30 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" C3' DT C 15 " pdb=" C4' DT C 15 " pdb=" O3' DT C 15 " pdb=" C2' DT C 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 1397 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 12 " 0.041 2.00e-02 2.50e+03 2.75e-02 1.71e+01 pdb=" N1 DC C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DC C 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC C 12 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DC C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC C 12 " 0.047 2.00e-02 2.50e+03 pdb=" N4 DC C 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC C 12 " -0.025 2.00e-02 2.50e+03 pdb=" C6 DC C 12 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 15 " -0.051 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" N1 DT C 15 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT C 15 " 0.018 2.00e-02 2.50e+03 pdb=" O2 DT C 15 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT C 15 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT C 15 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT C 15 " -0.026 2.00e-02 2.50e+03 pdb=" C5 DT C 15 " 0.013 2.00e-02 2.50e+03 pdb=" C7 DT C 15 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT C 15 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 30 " 0.019 2.00e-02 2.50e+03 2.07e-02 1.18e+01 pdb=" N9 DA B 30 " -0.053 2.00e-02 2.50e+03 pdb=" C8 DA B 30 " 0.037 2.00e-02 2.50e+03 pdb=" N7 DA B 30 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA B 30 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA B 30 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA B 30 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA B 30 " -0.006 2.00e-02 2.50e+03 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1501 2.76 - 3.30: 9795 3.30 - 3.83: 15952 3.83 - 4.37: 17791 4.37 - 4.90: 25995 Nonbonded interactions: 71034 Sorted by model distance: nonbonded pdb=" OG1 THR A 149 " pdb=" OE1 GLN A 179 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR D 149 " pdb=" OE1 GLN D 179 " model vdw 2.226 3.040 nonbonded pdb=" N ASP D 500 " pdb=" OD1 ASP D 500 " model vdw 2.239 3.120 nonbonded pdb=" N ASP A 500 " pdb=" OD1 ASP A 500 " model vdw 2.239 3.120 nonbonded pdb=" O VAL D 81 " pdb=" NE2 GLN D 455 " model vdw 2.244 3.120 ... (remaining 71029 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.180 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.008 0.053 8988 Z= 0.569 Angle : 1.029 11.585 12400 Z= 0.696 Chirality : 0.069 0.435 1400 Planarity : 0.007 0.066 1348 Dihedral : 22.029 179.364 3536 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.83 % Favored : 92.51 % Rotamer: Outliers : 0.49 % Allowed : 5.38 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.22), residues: 908 helix: -2.68 (0.18), residues: 438 sheet: -3.07 (0.55), residues: 60 loop : -3.19 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.008 ARG A 343 TYR 0.023 0.005 TYR A 174 PHE 0.028 0.003 PHE A 102 TRP 0.021 0.003 TRP D 41 HIS 0.015 0.003 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.57 ( 8988) covalent geometry : angle 1.02893 / 0.70 (12400) hydrogen bonds : bond 0.14250 / 8.84 ( 418) hydrogen bonds : angle 7.33435 / 5.26 ( 1184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8184 (mmm) cc_final: 0.7776 (mmp) REVERT: A 280 MET cc_start: 0.7800 (ppp) cc_final: 0.7234 (ppp) REVERT: A 337 ASP cc_start: 0.4447 (m-30) cc_final: 0.3873 (m-30) REVERT: D 193 GLU cc_start: 0.9063 (tp30) cc_final: 0.8540 (tp30) REVERT: D 197 MET cc_start: 0.8507 (mmm) cc_final: 0.7847 (mmp) REVERT: D 204 LEU cc_start: 0.8835 (pp) cc_final: 0.8560 (pt) REVERT: D 280 MET cc_start: 0.7380 (ppp) cc_final: 0.6939 (ppp) REVERT: D 337 ASP cc_start: 0.3946 (m-30) cc_final: 0.3736 (m-30) outliers start: 4 outliers final: 1 residues processed: 147 average time/residue: 0.1063 time to fit residues: 20.6319 Evaluate side-chains 90 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 166 ASN A 307 HIS D 115 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.124528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.094572 restraints weight = 28918.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.097991 restraints weight = 15185.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.100210 restraints weight = 9857.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.101608 restraints weight = 7338.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.102384 restraints weight = 6054.587| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8988 Z= 0.187 Angle : 0.763 7.112 12400 Z= 0.422 Chirality : 0.050 0.282 1400 Planarity : 0.005 0.047 1348 Dihedral : 25.466 179.452 1688 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.25), residues: 908 helix: -1.43 (0.22), residues: 456 sheet: -2.45 (0.57), residues: 54 loop : -2.63 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 445 TYR 0.018 0.002 TYR A 488 PHE 0.024 0.002 PHE A 347 TRP 0.011 0.002 TRP D 41 HIS 0.011 0.002 HIS D 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 8988) covalent geometry : angle 0.76262 / 0.42 (12400) hydrogen bonds : bond 0.05893 / 3.80 ( 418) hydrogen bonds : angle 5.86780 / 4.19 ( 1184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.7401 (mmp-170) cc_final: 0.6812 (tmt170) REVERT: A 146 ILE cc_start: 0.9028 (mm) cc_final: 0.8715 (mm) REVERT: A 176 ARG cc_start: 0.8868 (mtp85) cc_final: 0.7806 (mtp85) REVERT: A 197 MET cc_start: 0.8140 (mmm) cc_final: 0.7694 (mmp) REVERT: A 280 MET cc_start: 0.7905 (ppp) cc_final: 0.7397 (ppp) REVERT: A 310 LYS cc_start: 0.6869 (tppt) cc_final: 0.6497 (tppt) REVERT: A 443 ARG cc_start: 0.8777 (ttp-170) cc_final: 0.8564 (ttp80) REVERT: D 146 ILE cc_start: 0.8883 (mm) cc_final: 0.8572 (mm) REVERT: D 176 ARG cc_start: 0.8831 (mtp85) cc_final: 0.8067 (mtp85) REVERT: D 193 GLU cc_start: 0.9088 (tp30) cc_final: 0.8591 (tp30) REVERT: D 197 MET cc_start: 0.8584 (mmm) cc_final: 0.8275 (mmp) REVERT: D 204 LEU cc_start: 0.8851 (pp) cc_final: 0.8624 (pt) REVERT: D 280 MET cc_start: 0.7317 (ppp) cc_final: 0.6828 (ppp) REVERT: D 337 ASP cc_start: 0.4126 (m-30) cc_final: 0.3856 (m-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0991 time to fit residues: 17.8114 Evaluate side-chains 106 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 71 optimal weight: 0.0370 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.129982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.099041 restraints weight = 29859.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.102662 restraints weight = 15630.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.104972 restraints weight = 10107.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.106467 restraints weight = 7520.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.107324 restraints weight = 6166.575| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8988 Z= 0.151 Angle : 0.704 6.733 12400 Z= 0.390 Chirality : 0.049 0.265 1400 Planarity : 0.004 0.037 1348 Dihedral : 25.391 178.252 1688 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.12 % Allowed : 2.81 % Favored : 97.07 % 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: -2.42 (0.26), residues: 908 helix: -0.98 (0.22), residues: 456 sheet: -1.85 (0.62), residues: 52 loop : -2.25 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 309 TYR 0.022 0.002 TYR A 402 PHE 0.045 0.002 PHE A 102 TRP 0.014 0.002 TRP D 400 HIS 0.006 0.001 HIS D 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 8988) covalent geometry : angle 0.70400 / 0.39 (12400) hydrogen bonds : bond 0.04852 / 3.16 ( 418) hydrogen bonds : angle 5.42467 / 3.88 ( 1184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8847 (tp) cc_final: 0.8621 (tt) REVERT: A 36 LEU cc_start: 0.9056 (mp) cc_final: 0.8850 (mp) REVERT: A 73 TYR cc_start: 0.8617 (m-10) cc_final: 0.8305 (m-80) REVERT: A 146 ILE cc_start: 0.9037 (mm) cc_final: 0.8772 (mm) REVERT: A 176 ARG cc_start: 0.8708 (mtp85) cc_final: 0.7649 (mtp85) REVERT: A 197 MET cc_start: 0.8120 (mmm) cc_final: 0.7683 (mmp) REVERT: A 280 MET cc_start: 0.7925 (ppp) cc_final: 0.7442 (ppp) REVERT: A 310 LYS cc_start: 0.6898 (tppt) cc_final: 0.6579 (tppt) REVERT: A 337 ASP cc_start: 0.4838 (m-30) cc_final: 0.4571 (m-30) REVERT: D 106 ARG cc_start: 0.8193 (mmp-170) cc_final: 0.7375 (tmt170) REVERT: D 146 ILE cc_start: 0.8892 (mm) cc_final: 0.8580 (mm) REVERT: D 152 VAL cc_start: 0.9310 (t) cc_final: 0.9101 (t) REVERT: D 193 GLU cc_start: 0.9120 (tp30) cc_final: 0.8614 (tp30) REVERT: D 197 MET cc_start: 0.8636 (mmm) cc_final: 0.8112 (mmp) REVERT: D 219 MET cc_start: 0.7761 (mmm) cc_final: 0.7518 (mmp) REVERT: D 280 MET cc_start: 0.7122 (ppp) cc_final: 0.6691 (tpp) REVERT: D 464 MET cc_start: 0.8903 (tpt) cc_final: 0.8378 (tpp) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.0898 time to fit residues: 17.6463 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.0030 chunk 8 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.130348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.099881 restraints weight = 30920.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.103389 restraints weight = 16382.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.105653 restraints weight = 10690.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.107106 restraints weight = 7971.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.108020 restraints weight = 6569.745| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8988 Z= 0.139 Angle : 0.664 5.951 12400 Z= 0.368 Chirality : 0.047 0.265 1400 Planarity : 0.004 0.038 1348 Dihedral : 25.128 177.950 1688 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.27), residues: 908 helix: -0.61 (0.23), residues: 458 sheet: -1.73 (0.62), residues: 52 loop : -2.04 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 443 TYR 0.025 0.002 TYR D 401 PHE 0.033 0.002 PHE D 102 TRP 0.029 0.002 TRP D 400 HIS 0.005 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 8988) covalent geometry : angle 0.66449 / 0.37 (12400) hydrogen bonds : bond 0.04495 / 2.94 ( 418) hydrogen bonds : angle 5.06914 / 3.64 ( 1184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8779 (tp) cc_final: 0.8491 (tt) REVERT: A 36 LEU cc_start: 0.9060 (mp) cc_final: 0.8841 (mp) REVERT: A 146 ILE cc_start: 0.9086 (mm) cc_final: 0.8794 (mm) REVERT: A 176 ARG cc_start: 0.8690 (mtp85) cc_final: 0.7805 (mtp85) REVERT: A 280 MET cc_start: 0.7933 (ppp) cc_final: 0.7432 (ppp) REVERT: A 310 LYS cc_start: 0.6871 (tppt) cc_final: 0.6585 (tppt) REVERT: A 467 ILE cc_start: 0.9369 (mt) cc_final: 0.9167 (tp) REVERT: D 106 ARG cc_start: 0.8197 (mmp-170) cc_final: 0.7565 (tmt170) REVERT: D 124 PHE cc_start: 0.9198 (p90) cc_final: 0.8926 (p90) REVERT: D 146 ILE cc_start: 0.8933 (mm) cc_final: 0.8640 (mm) REVERT: D 197 MET cc_start: 0.8710 (mmm) cc_final: 0.8186 (mmp) REVERT: D 219 MET cc_start: 0.7936 (mmm) cc_final: 0.7622 (mmp) REVERT: D 280 MET cc_start: 0.6978 (ppp) cc_final: 0.6594 (tpp) REVERT: D 401 TYR cc_start: 0.8338 (t80) cc_final: 0.8064 (t80) REVERT: D 467 ILE cc_start: 0.9401 (mt) cc_final: 0.9174 (tp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0897 time to fit residues: 16.4538 Evaluate side-chains 112 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 0.0050 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.098852 restraints weight = 30589.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.102379 restraints weight = 16072.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.104677 restraints weight = 10462.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.106057 restraints weight = 7809.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.107082 restraints weight = 6468.429| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.151 Angle : 0.657 5.784 12400 Z= 0.365 Chirality : 0.047 0.272 1400 Planarity : 0.004 0.054 1348 Dihedral : 24.984 177.699 1688 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -1.74 (0.27), residues: 908 helix: -0.32 (0.24), residues: 452 sheet: -1.54 (0.63), residues: 54 loop : -2.04 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 106 TYR 0.016 0.002 TYR D 401 PHE 0.029 0.002 PHE A 102 TRP 0.013 0.001 TRP A 400 HIS 0.006 0.001 HIS D 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 ( 8988) covalent geometry : angle 0.65748 / 0.37 (12400) hydrogen bonds : bond 0.04405 / 2.88 ( 418) hydrogen bonds : angle 5.01117 / 3.58 ( 1184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8790 (tp) cc_final: 0.8531 (tt) REVERT: A 36 LEU cc_start: 0.9067 (mp) cc_final: 0.8833 (mp) REVERT: A 124 PHE cc_start: 0.9234 (p90) cc_final: 0.8985 (p90) REVERT: A 146 ILE cc_start: 0.9091 (mm) cc_final: 0.8840 (mm) REVERT: A 176 ARG cc_start: 0.8722 (mtp85) cc_final: 0.7954 (mtp85) REVERT: A 233 GLU cc_start: 0.6600 (mp0) cc_final: 0.6176 (tm-30) REVERT: A 280 MET cc_start: 0.7918 (ppp) cc_final: 0.7421 (ppp) REVERT: A 310 LYS cc_start: 0.6952 (tppt) cc_final: 0.6666 (tppt) REVERT: A 464 MET cc_start: 0.9098 (ttm) cc_final: 0.8469 (ttm) REVERT: D 124 PHE cc_start: 0.9178 (p90) cc_final: 0.8857 (p90) REVERT: D 146 ILE cc_start: 0.8944 (mm) cc_final: 0.8681 (mm) REVERT: D 197 MET cc_start: 0.8670 (mmm) cc_final: 0.8129 (mmp) REVERT: D 219 MET cc_start: 0.7830 (mmm) cc_final: 0.7521 (mmp) REVERT: D 280 MET cc_start: 0.7014 (ppp) cc_final: 0.6695 (tpp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0825 time to fit residues: 15.3395 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 18 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.130785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.100028 restraints weight = 30672.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.103585 restraints weight = 16559.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.105884 restraints weight = 10848.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.107360 restraints weight = 8142.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.108330 restraints weight = 6742.614| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8988 Z= 0.139 Angle : 0.642 5.699 12400 Z= 0.357 Chirality : 0.046 0.272 1400 Planarity : 0.004 0.038 1348 Dihedral : 24.871 177.263 1688 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.62 (0.27), residues: 908 helix: -0.18 (0.24), residues: 450 sheet: -1.39 (0.67), residues: 54 loop : -2.05 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.027 0.002 TYR A 73 PHE 0.039 0.002 PHE A 444 TRP 0.022 0.002 TRP D 400 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 ( 8988) covalent geometry : angle 0.64195 / 0.36 (12400) hydrogen bonds : bond 0.04244 / 2.76 ( 418) hydrogen bonds : angle 4.90114 / 3.54 ( 1184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8900 (tp) cc_final: 0.8626 (tt) REVERT: A 36 LEU cc_start: 0.9083 (mp) cc_final: 0.8858 (mp) REVERT: A 115 GLN cc_start: 0.8419 (pt0) cc_final: 0.7955 (tp40) REVERT: A 146 ILE cc_start: 0.9079 (mm) cc_final: 0.8836 (mm) REVERT: A 176 ARG cc_start: 0.8652 (mtp85) cc_final: 0.7931 (mtp85) REVERT: A 233 GLU cc_start: 0.6574 (mp0) cc_final: 0.6024 (tm-30) REVERT: A 280 MET cc_start: 0.7743 (ppp) cc_final: 0.7200 (ppp) REVERT: A 310 LYS cc_start: 0.6955 (tppt) cc_final: 0.6679 (tppt) REVERT: A 337 ASP cc_start: 0.4782 (m-30) cc_final: 0.4572 (m-30) REVERT: A 464 MET cc_start: 0.9026 (ttm) cc_final: 0.8171 (ttp) REVERT: D 146 ILE cc_start: 0.8858 (mm) cc_final: 0.8588 (mm) REVERT: D 197 MET cc_start: 0.8659 (mmm) cc_final: 0.8075 (mmp) REVERT: D 219 MET cc_start: 0.7558 (mmm) cc_final: 0.7353 (mmp) REVERT: D 280 MET cc_start: 0.7221 (ppp) cc_final: 0.6952 (tpp) REVERT: D 464 MET cc_start: 0.9050 (ttm) cc_final: 0.8299 (ttp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0912 time to fit residues: 16.9747 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.100211 restraints weight = 30763.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.103886 restraints weight = 16030.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.106265 restraints weight = 10410.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.107793 restraints weight = 7778.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.108658 restraints weight = 6412.683| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.137 Angle : 0.656 9.262 12400 Z= 0.359 Chirality : 0.046 0.273 1400 Planarity : 0.004 0.041 1348 Dihedral : 24.776 177.046 1688 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.53 (0.27), residues: 908 helix: -0.10 (0.24), residues: 450 sheet: -1.33 (0.66), residues: 52 loop : -2.01 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.044 0.002 TYR A 73 PHE 0.043 0.002 PHE A 444 TRP 0.020 0.002 TRP D 400 HIS 0.004 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 ( 8988) covalent geometry : angle 0.65642 / 0.36 (12400) hydrogen bonds : bond 0.04083 / 2.68 ( 418) hydrogen bonds : angle 4.84201 / 3.49 ( 1184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8908 (tp) cc_final: 0.8644 (tt) REVERT: A 36 LEU cc_start: 0.9073 (mp) cc_final: 0.8860 (mp) REVERT: A 146 ILE cc_start: 0.9128 (mm) cc_final: 0.8904 (mm) REVERT: A 176 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8000 (mtp85) REVERT: A 233 GLU cc_start: 0.6489 (mp0) cc_final: 0.5998 (tm-30) REVERT: A 280 MET cc_start: 0.7672 (ppp) cc_final: 0.7103 (ppp) REVERT: A 310 LYS cc_start: 0.6975 (tppt) cc_final: 0.6694 (tppt) REVERT: D 146 ILE cc_start: 0.8826 (mm) cc_final: 0.8588 (mm) REVERT: D 152 VAL cc_start: 0.9333 (t) cc_final: 0.9119 (t) REVERT: D 197 MET cc_start: 0.8643 (mmm) cc_final: 0.8057 (mmp) REVERT: D 219 MET cc_start: 0.7668 (mmm) cc_final: 0.7422 (mmp) REVERT: D 280 MET cc_start: 0.7066 (ppp) cc_final: 0.6758 (tpp) REVERT: D 344 PHE cc_start: 0.5647 (m-80) cc_final: 0.5231 (m-80) REVERT: D 416 ASP cc_start: 0.7990 (t0) cc_final: 0.7586 (p0) REVERT: D 444 PHE cc_start: 0.8476 (m-10) cc_final: 0.8274 (m-80) REVERT: D 464 MET cc_start: 0.9004 (ttm) cc_final: 0.8675 (ttm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0851 time to fit residues: 16.5337 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.132093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.100556 restraints weight = 30058.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.104258 restraints weight = 16020.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.106642 restraints weight = 10464.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.108154 restraints weight = 7832.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.109183 restraints weight = 6472.236| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8988 Z= 0.130 Angle : 0.634 6.580 12400 Z= 0.352 Chirality : 0.045 0.267 1400 Planarity : 0.004 0.046 1348 Dihedral : 24.708 176.620 1688 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -1.48 (0.28), residues: 908 helix: -0.11 (0.24), residues: 454 sheet: -1.48 (0.67), residues: 56 loop : -1.91 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.033 0.001 TYR A 73 PHE 0.039 0.002 PHE A 444 TRP 0.016 0.001 TRP D 400 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 8988) covalent geometry : angle 0.63413 / 0.35 (12400) hydrogen bonds : bond 0.03899 / 2.54 ( 418) hydrogen bonds : angle 4.73688 / 3.41 ( 1184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8858 (tp) cc_final: 0.8608 (tt) REVERT: A 36 LEU cc_start: 0.9082 (mp) cc_final: 0.8840 (mp) REVERT: A 176 ARG cc_start: 0.8757 (mtp85) cc_final: 0.7893 (mtp85) REVERT: A 233 GLU cc_start: 0.6510 (mp0) cc_final: 0.6151 (tm-30) REVERT: A 280 MET cc_start: 0.7768 (ppp) cc_final: 0.7356 (ppp) REVERT: A 310 LYS cc_start: 0.6838 (tppt) cc_final: 0.6551 (tppt) REVERT: A 359 GLU cc_start: 0.6649 (mp0) cc_final: 0.5504 (tm-30) REVERT: A 446 GLU cc_start: 0.8601 (tt0) cc_final: 0.8304 (mm-30) REVERT: A 464 MET cc_start: 0.8841 (ttm) cc_final: 0.8398 (ttm) REVERT: A 472 LEU cc_start: 0.8900 (tp) cc_final: 0.8595 (tp) REVERT: D 106 ARG cc_start: 0.8120 (mmp-170) cc_final: 0.7768 (tmt170) REVERT: D 146 ILE cc_start: 0.8918 (mm) cc_final: 0.8654 (mm) REVERT: D 161 ASP cc_start: 0.7635 (p0) cc_final: 0.6487 (m-30) REVERT: D 197 MET cc_start: 0.8648 (mmm) cc_final: 0.8043 (mmp) REVERT: D 219 MET cc_start: 0.7650 (mmm) cc_final: 0.7427 (mmp) REVERT: D 233 GLU cc_start: 0.7083 (mp0) cc_final: 0.5917 (tm-30) REVERT: D 280 MET cc_start: 0.6986 (ppp) cc_final: 0.6754 (tpp) REVERT: D 344 PHE cc_start: 0.5793 (m-80) cc_final: 0.5464 (m-80) REVERT: D 416 ASP cc_start: 0.7946 (t0) cc_final: 0.7539 (p0) REVERT: D 464 MET cc_start: 0.9109 (ttm) cc_final: 0.8773 (ttm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0811 time to fit residues: 15.0247 Evaluate side-chains 102 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.0170 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.130127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.098690 restraints weight = 30682.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.102253 restraints weight = 16470.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.104525 restraints weight = 10860.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106009 restraints weight = 8194.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.106828 restraints weight = 6807.795| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8988 Z= 0.182 Angle : 0.688 6.915 12400 Z= 0.377 Chirality : 0.047 0.277 1400 Planarity : 0.005 0.060 1348 Dihedral : 24.629 177.466 1688 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.27), residues: 908 helix: -0.13 (0.24), residues: 450 sheet: -1.81 (0.63), residues: 54 loop : -1.84 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 106 TYR 0.032 0.002 TYR A 73 PHE 0.033 0.002 PHE A 444 TRP 0.015 0.002 TRP D 400 HIS 0.006 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 8988) covalent geometry : angle 0.68837 / 0.38 (12400) hydrogen bonds : bond 0.04289 / 2.78 ( 418) hydrogen bonds : angle 4.86311 / 3.50 ( 1184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8906 (tp) cc_final: 0.8663 (tt) REVERT: A 36 LEU cc_start: 0.9088 (mp) cc_final: 0.8855 (mp) REVERT: A 103 GLU cc_start: 0.8028 (pp20) cc_final: 0.7794 (pp20) REVERT: A 280 MET cc_start: 0.7717 (ppp) cc_final: 0.7256 (ppp) REVERT: A 310 LYS cc_start: 0.6863 (tppt) cc_final: 0.6567 (tppt) REVERT: A 359 GLU cc_start: 0.6758 (mp0) cc_final: 0.5580 (tm-30) REVERT: A 464 MET cc_start: 0.8860 (ttm) cc_final: 0.8094 (ttp) REVERT: A 488 TYR cc_start: 0.5391 (m-10) cc_final: 0.4851 (m-10) REVERT: D 146 ILE cc_start: 0.8958 (mm) cc_final: 0.8702 (mm) REVERT: D 161 ASP cc_start: 0.7399 (p0) cc_final: 0.6697 (m-30) REVERT: D 197 MET cc_start: 0.8704 (mmm) cc_final: 0.8053 (mmp) REVERT: D 219 MET cc_start: 0.7722 (mmm) cc_final: 0.7491 (mmp) REVERT: D 233 GLU cc_start: 0.7135 (mp0) cc_final: 0.5890 (tm-30) REVERT: D 416 ASP cc_start: 0.7992 (t0) cc_final: 0.7563 (p0) REVERT: D 464 MET cc_start: 0.9118 (ttm) cc_final: 0.8271 (ttp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0883 time to fit residues: 15.8644 Evaluate side-chains 98 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 14 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.132613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.101499 restraints weight = 30265.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.105224 restraints weight = 16176.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.107614 restraints weight = 10510.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.109132 restraints weight = 7843.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.110086 restraints weight = 6471.471| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8988 Z= 0.130 Angle : 0.662 8.741 12400 Z= 0.360 Chirality : 0.048 0.390 1400 Planarity : 0.004 0.044 1348 Dihedral : 24.582 176.583 1688 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.46 (0.27), residues: 908 helix: -0.09 (0.24), residues: 454 sheet: -1.28 (0.68), residues: 54 loop : -1.94 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 106 TYR 0.018 0.001 TYR A 73 PHE 0.038 0.002 PHE A 444 TRP 0.014 0.002 TRP D 400 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 8988) covalent geometry : angle 0.66223 / 0.36 (12400) hydrogen bonds : bond 0.03760 / 2.45 ( 418) hydrogen bonds : angle 4.66468 / 3.37 ( 1184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8857 (tp) cc_final: 0.8622 (tt) REVERT: A 36 LEU cc_start: 0.9069 (mp) cc_final: 0.8852 (mp) REVERT: A 176 ARG cc_start: 0.8761 (mtp85) cc_final: 0.7919 (mtp85) REVERT: A 233 GLU cc_start: 0.6674 (mp0) cc_final: 0.5814 (tm-30) REVERT: A 280 MET cc_start: 0.7671 (ppp) cc_final: 0.7259 (ppp) REVERT: A 359 GLU cc_start: 0.6765 (mp0) cc_final: 0.5648 (tm-30) REVERT: A 464 MET cc_start: 0.8772 (ttm) cc_final: 0.8335 (ttm) REVERT: A 488 TYR cc_start: 0.5202 (m-10) cc_final: 0.4698 (m-10) REVERT: D 30 LEU cc_start: 0.9060 (tp) cc_final: 0.8779 (tp) REVERT: D 106 ARG cc_start: 0.7714 (mmp-170) cc_final: 0.7338 (tmt170) REVERT: D 121 LYS cc_start: 0.8091 (ptpt) cc_final: 0.7809 (ptpt) REVERT: D 146 ILE cc_start: 0.8908 (mm) cc_final: 0.8621 (mm) REVERT: D 152 VAL cc_start: 0.9279 (t) cc_final: 0.9077 (t) REVERT: D 161 ASP cc_start: 0.7045 (p0) cc_final: 0.6323 (m-30) REVERT: D 176 ARG cc_start: 0.8724 (mtp85) cc_final: 0.7799 (mtp85) REVERT: D 197 MET cc_start: 0.8624 (mmm) cc_final: 0.8017 (mmp) REVERT: D 233 GLU cc_start: 0.6910 (mp0) cc_final: 0.5968 (tm-30) REVERT: D 416 ASP cc_start: 0.7985 (t0) cc_final: 0.7571 (p0) REVERT: D 444 PHE cc_start: 0.8469 (m-10) cc_final: 0.8133 (m-80) REVERT: D 464 MET cc_start: 0.9062 (ttm) cc_final: 0.8750 (ttm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0893 time to fit residues: 16.4737 Evaluate side-chains 105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 0.0040 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.100228 restraints weight = 30297.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.103896 restraints weight = 16219.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.106227 restraints weight = 10582.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.107754 restraints weight = 7932.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.108649 restraints weight = 6546.853| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8988 Z= 0.138 Angle : 0.651 6.483 12400 Z= 0.357 Chirality : 0.047 0.337 1400 Planarity : 0.004 0.043 1348 Dihedral : 24.552 177.323 1688 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.37 (0.27), residues: 908 helix: -0.02 (0.24), residues: 454 sheet: -1.46 (0.65), residues: 52 loop : -1.86 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 106 TYR 0.029 0.001 TYR A 73 PHE 0.048 0.002 PHE A 102 TRP 0.014 0.002 TRP D 400 HIS 0.004 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 8988) covalent geometry : angle 0.65070 / 0.36 (12400) hydrogen bonds : bond 0.03877 / 2.51 ( 418) hydrogen bonds : angle 4.72338 / 3.44 ( 1184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.58 seconds wall clock time: 28 minutes 0.64 seconds (1680.64 seconds total)