Starting phenix.real_space_refine on Fri Sep 11 14:43:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pqx_20455/09_2026/6pqx_20455.cif" } resolution = 4.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 120 5.49 5 S 36 5.16 5 C 6036 2.51 5 N 1758 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.00s 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: 10116 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3826 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3826 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 10116 At special positions: 0 Unit cell: (106.05, 89.25, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 36 16.00 P 120 15.00 O 2162 8.00 N 1758 7.00 C 6036 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: 0.90 Conformation dependent library (CDL) restraints added in 312.3 milliseconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 57.3% alpha, 13.8% beta 50 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.504A pdb=" N CYS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.925A pdb=" N GLU A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.673A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 224 through 232 removed outlier: 4.664A pdb=" N TYR A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.754A pdb=" N SER A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 271 through 290 removed outlier: 3.830A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.879A pdb=" N ASP A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 4.281A pdb=" N PHE A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 4.179A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.715A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.617A pdb=" N ARG A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'E' and resid 25 through 37 Processing helix chain 'E' and resid 39 through 53 Processing helix chain 'E' and resid 61 through 73 removed outlier: 3.504A pdb=" N CYS E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 105 removed outlier: 3.925A pdb=" N GLU E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.673A pdb=" N TYR E 174 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 224 through 232 removed outlier: 4.663A pdb=" N TYR E 230 " --> pdb=" O LYS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.755A pdb=" N SER E 251 " --> pdb=" O PRO E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 271 through 290 removed outlier: 3.831A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 322 removed outlier: 3.879A pdb=" N ASP E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 4.280A pdb=" N PHE E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 removed outlier: 4.179A pdb=" N THR E 351 " --> pdb=" O PHE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.716A pdb=" N ILE E 362 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 413 through 421 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.618A pdb=" N ARG E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 470 through 476 Processing helix chain 'E' and resid 489 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 164 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 119 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 156 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 117 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 116 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A 124 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP E 164 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE E 119 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 156 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE E 117 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU E 116 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE E 124 " --> pdb=" O THR E 221 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.21 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: 2498 1.33 - 1.45: 2517 1.45 - 1.57: 5247 1.57 - 1.69: 234 1.69 - 1.81: 56 Bond restraints: 10552 Sorted by residual: bond pdb=" C3' DG H 16 " pdb=" C2' DG H 16 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.07e+01 bond pdb=" C3' DG D 16 " pdb=" C2' DG D 16 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.05e+01 bond pdb=" O3' DA H 19 " pdb=" P DT H 20 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.20e-02 6.94e+03 1.87e+01 bond pdb=" O3' DC D 5 " pdb=" P DG D 6 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.20e-02 6.94e+03 1.86e+01 bond pdb=" O3' DA H 11 " pdb=" P DC H 12 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.20e-02 6.94e+03 1.74e+01 ... (remaining 10547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 14161 2.47 - 4.94: 536 4.94 - 7.42: 56 7.42 - 9.89: 4 9.89 - 12.36: 1 Bond angle restraints: 14758 Sorted by residual: angle pdb=" O5' DA D 28 " pdb=" C5' DA D 28 " pdb=" C4' DA D 28 " ideal model delta sigma weight residual 109.40 115.30 -5.90 8.00e-01 1.56e+00 5.44e+01 angle pdb=" O5' DA H 28 " pdb=" C5' DA H 28 " pdb=" C4' DA H 28 " ideal model delta sigma weight residual 109.40 115.24 -5.84 8.00e-01 1.56e+00 5.33e+01 angle pdb=" O5' DC D 12 " pdb=" C5' DC D 12 " pdb=" C4' DC D 12 " ideal model delta sigma weight residual 109.40 114.12 -4.72 8.00e-01 1.56e+00 3.48e+01 angle pdb=" O5' DT H 20 " pdb=" C5' DT H 20 " pdb=" C4' DT H 20 " ideal model delta sigma weight residual 109.40 114.10 -4.70 8.00e-01 1.56e+00 3.45e+01 angle pdb=" O5' DT D 20 " pdb=" C5' DT D 20 " pdb=" C4' DT D 20 " ideal model delta sigma weight residual 109.40 113.61 -4.21 8.00e-01 1.56e+00 2.76e+01 ... (remaining 14753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4748 17.40 - 34.79: 681 34.79 - 52.19: 405 52.19 - 69.58: 230 69.58 - 86.98: 26 Dihedral angle restraints: 6090 sinusoidal: 3262 harmonic: 2828 Sorted by residual: dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N PRO A 60 " pdb=" CA PRO A 60 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA TYR E 59 " pdb=" C TYR E 59 " pdb=" N PRO E 60 " pdb=" CA PRO E 60 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN E 135 " pdb=" C GLN E 135 " pdb=" N ASN E 136 " pdb=" CA ASN E 136 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1357 0.075 - 0.150: 281 0.150 - 0.225: 30 0.225 - 0.300: 3 0.300 - 0.374: 3 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C3' DC H 5 " pdb=" C4' DC H 5 " pdb=" O3' DC H 5 " pdb=" C2' DC H 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C4' DA H 28 " pdb=" C5' DA H 28 " pdb=" O4' DA H 28 " pdb=" C3' DA H 28 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C4' DA D 28 " pdb=" C5' DA D 28 " pdb=" O4' DA D 28 " pdb=" C3' DA D 28 " both_signs ideal model delta sigma weight residual False -2.53 -2.19 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 1671 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC D 12 " 0.028 2.00e-02 2.50e+03 3.80e-02 3.25e+01 pdb=" N1 DC D 12 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DC D 12 " -0.041 2.00e-02 2.50e+03 pdb=" O2 DC D 12 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DC D 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC D 12 " -0.069 2.00e-02 2.50e+03 pdb=" N4 DC D 12 " 0.072 2.00e-02 2.50e+03 pdb=" C5 DC D 12 " -0.014 2.00e-02 2.50e+03 pdb=" C6 DC D 12 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C 29 " 0.017 2.00e-02 2.50e+03 3.07e-02 2.60e+01 pdb=" N9 DA C 29 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DA C 29 " 0.029 2.00e-02 2.50e+03 pdb=" N7 DA C 29 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA C 29 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA C 29 " 0.016 2.00e-02 2.50e+03 pdb=" N6 DA C 29 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA C 29 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DA C 29 " 0.055 2.00e-02 2.50e+03 pdb=" N3 DA C 29 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA C 29 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 29 " 0.008 2.00e-02 2.50e+03 3.05e-02 2.56e+01 pdb=" N9 DA G 29 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA G 29 " 0.030 2.00e-02 2.50e+03 pdb=" N7 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA G 29 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DA G 29 " 0.053 2.00e-02 2.50e+03 pdb=" N6 DA G 29 " -0.045 2.00e-02 2.50e+03 pdb=" N1 DA G 29 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA G 29 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DA G 29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA G 29 " -0.059 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1872 2.77 - 3.30: 10898 3.30 - 3.83: 19166 3.83 - 4.37: 21913 4.37 - 4.90: 32435 Nonbonded interactions: 86284 Sorted by model distance: nonbonded pdb=" NE ARG A 342 " pdb=" OP1 DA C 18 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG E 485 " pdb=" OP1 DC G 17 " model vdw 2.243 3.120 nonbonded pdb=" O GLY A 126 " pdb="CA CA A 601 " model vdw 2.259 2.510 nonbonded pdb=" O ASP A 188 " pdb=" ND2 ASN A 192 " model vdw 2.260 3.120 nonbonded pdb=" O ASP E 188 " pdb=" ND2 ASN E 192 " model vdw 2.261 3.120 ... (remaining 86279 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 0.590 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: 0.030 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10552 Z= 0.522 Angle : 1.052 12.362 14758 Z= 0.745 Chirality : 0.062 0.374 1674 Planarity : 0.008 0.093 1450 Dihedral : 23.408 86.978 4254 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.23 % Favored : 94.14 % Rotamer: Outliers : 2.35 % Allowed : 3.87 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.41 (0.21), residues: 956 helix: -2.19 (0.17), residues: 482 sheet: -1.76 (0.57), residues: 64 loop : -2.29 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.007 ARG A 437 TYR 0.020 0.005 TYR A 59 PHE 0.028 0.002 PHE A 317 TRP 0.027 0.003 TRP A 41 HIS 0.009 0.002 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.52 (10552) covalent geometry : angle 1.05211 / 0.74 (14758) hydrogen bonds : bond 0.16704 / 10.47 ( 521) hydrogen bonds : angle 7.21869 / 5.02 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8526 (mm) REVERT: A 145 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.6849 (p) REVERT: A 169 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8106 (Cg_endo) REVERT: A 201 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9005 (tt) REVERT: A 220 MET cc_start: 0.7639 (tmm) cc_final: 0.6949 (tmm) REVERT: A 250 MET cc_start: 0.8661 (ttm) cc_final: 0.7668 (ttm) REVERT: A 344 PHE cc_start: 0.8858 (t80) cc_final: 0.8504 (t80) REVERT: A 364 ARG cc_start: 0.8466 (mtp85) cc_final: 0.7943 (mtp180) REVERT: A 403 MET cc_start: 0.7867 (pmm) cc_final: 0.6994 (pmm) REVERT: A 437 ARG cc_start: 0.8945 (tpp-160) cc_final: 0.8420 (tpp80) outliers start: 10 outliers final: 2 residues processed: 99 average time/residue: 0.0770 time to fit residues: 9.2381 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0087 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0087 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 overall best weight: 2.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076850 restraints weight = 15186.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078930 restraints weight = 9634.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080379 restraints weight = 6608.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081423 restraints weight = 4875.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082201 restraints weight = 3784.489| |-----------------------------------------------------------------------------| r_work (final): 0.3292 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.111629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.110128 restraints weight = 3121.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110789 restraints weight = 1089.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.111067 restraints weight = 495.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.111067 restraints weight = 280.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.111067 restraints weight = 280.577| |-----------------------------------------------------------------------------| r_work (final): 0.3933 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070663 restraints weight = 3042.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071612 restraints weight = 1011.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072155 restraints weight = 453.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072473 restraints weight = 256.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072596 restraints weight = 170.998| |-----------------------------------------------------------------------------| r_work (final): 0.3159 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.091398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.084551 restraints weight = 6612.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085227 restraints weight = 2604.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085625 restraints weight = 1672.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085740 restraints weight = 1378.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085740 restraints weight = 1302.347| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10552 Z= 0.190 Angle : 0.817 9.580 14758 Z= 0.444 Chirality : 0.046 0.204 1674 Planarity : 0.006 0.058 1450 Dihedral : 27.851 89.550 2342 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.39 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -2.16 (0.24), residues: 956 helix: -1.02 (0.21), residues: 496 sheet: -1.44 (0.53), residues: 72 loop : -1.84 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 443 TYR 0.018 0.002 TYR E 488 PHE 0.019 0.002 PHE A 344 TRP 0.018 0.002 TRP E 41 HIS 0.006 0.002 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (10552) covalent geometry : angle 0.81716 / 0.44 (14758) hydrogen bonds : bond 0.10696 / 7.10 ( 521) hydrogen bonds : angle 5.92726 / 4.08 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 119 ILE cc_start: 0.9021 (pt) cc_final: 0.8726 (mm) REVERT: E 220 MET cc_start: 0.7739 (tmm) cc_final: 0.7316 (tmm) REVERT: E 250 MET cc_start: 0.8730 (ttm) cc_final: 0.7825 (ttm) REVERT: E 282 CYS cc_start: 0.8688 (p) cc_final: 0.8446 (p) REVERT: E 344 PHE cc_start: 0.8717 (t80) cc_final: 0.8363 (t80) REVERT: E 364 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7541 (mtm-85) REVERT: E 403 MET cc_start: 0.7976 (pmm) cc_final: 0.7139 (pmm) REVERT: E 439 LYS cc_start: 0.8452 (tttt) cc_final: 0.8145 (tptt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0824 time to fit residues: 7.5838 Evaluate side-chains 51 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.160 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0054 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0086 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 105 optimal weight: 40.0000 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 0.0010 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076026 restraints weight = 14944.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077964 restraints weight = 9175.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079367 restraints weight = 6265.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080336 restraints weight = 4581.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081148 restraints weight = 3555.536| |-----------------------------------------------------------------------------| r_work (final): 0.3283 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.102952 restraints weight = 2968.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.103918 restraints weight = 1495.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.104462 restraints weight = 1140.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.104620 restraints weight = 980.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.104620 restraints weight = 934.182| |-----------------------------------------------------------------------------| r_work (final): 0.3804 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.072791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070325 restraints weight = 3075.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071136 restraints weight = 1056.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071530 restraints weight = 473.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.071820 restraints weight = 290.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071975 restraints weight = 192.718| |-----------------------------------------------------------------------------| r_work (final): 0.3188 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.092782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082955 restraints weight = 5859.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.082720 restraints weight = 3151.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083019 restraints weight = 2815.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082858 restraints weight = 2302.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082979 restraints weight = 2149.540| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10552 Z= 0.223 Angle : 0.784 8.110 14758 Z= 0.435 Chirality : 0.046 0.223 1674 Planarity : 0.006 0.061 1450 Dihedral : 27.816 86.977 2342 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.23 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -1.65 (0.26), residues: 956 helix: -0.57 (0.22), residues: 498 sheet: -1.00 (0.57), residues: 72 loop : -1.71 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 364 TYR 0.011 0.002 TYR E 241 PHE 0.037 0.002 PHE A 344 TRP 0.012 0.002 TRP A 41 HIS 0.007 0.002 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (10552) covalent geometry : angle 0.78422 / 0.43 (14758) hydrogen bonds : bond 0.10287 / 6.92 ( 521) hydrogen bonds : angle 5.61741 / 3.85 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.152 Fit side-chains REVERT: E 119 ILE cc_start: 0.8993 (pt) cc_final: 0.8671 (mm) REVERT: E 173 MET cc_start: 0.8788 (mtp) cc_final: 0.8485 (ttm) REVERT: E 250 MET cc_start: 0.8682 (ttm) cc_final: 0.7819 (ttm) REVERT: E 337 ASP cc_start: 0.7819 (p0) cc_final: 0.6404 (t0) REVERT: E 364 ARG cc_start: 0.8456 (mtp85) cc_final: 0.7556 (mtm-85) REVERT: E 370 GLN cc_start: 0.8541 (mt0) cc_final: 0.8217 (tp40) REVERT: E 403 MET cc_start: 0.8101 (pmm) cc_final: 0.7222 (pmm) REVERT: E 409 LYS cc_start: 0.9000 (ptmt) cc_final: 0.8540 (pttm) REVERT: E 439 LYS cc_start: 0.8473 (tttt) cc_final: 0.8239 (tptt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0584 time to fit residues: 5.1437 Evaluate side-chains 50 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.091 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0078 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 83 optimal weight: 0.0670 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.078179 restraints weight = 14511.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.080302 restraints weight = 8832.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081837 restraints weight = 5934.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082930 restraints weight = 4269.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083591 restraints weight = 3270.515| |-----------------------------------------------------------------------------| r_work (final): 0.3338 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.110798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102720 restraints weight = 3068.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103867 restraints weight = 1553.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104492 restraints weight = 1107.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.104617 restraints weight = 972.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.104767 restraints weight = 926.304| |-----------------------------------------------------------------------------| r_work (final): 0.3831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.076448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073246 restraints weight = 2611.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074458 restraints weight = 1143.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074908 restraints weight = 580.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075399 restraints weight = 399.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075657 restraints weight = 251.503| |-----------------------------------------------------------------------------| r_work (final): 0.3222 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.093228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.087072 restraints weight = 5837.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087661 restraints weight = 2484.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087669 restraints weight = 1828.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087842 restraints weight = 1812.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087842 restraints weight = 1692.264| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10552 Z= 0.149 Angle : 0.707 7.342 14758 Z= 0.393 Chirality : 0.044 0.190 1674 Planarity : 0.005 0.052 1450 Dihedral : 27.693 84.397 2342 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.26), residues: 956 helix: -0.10 (0.22), residues: 498 sheet: -0.71 (0.63), residues: 62 loop : -1.67 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 485 TYR 0.023 0.002 TYR A 398 PHE 0.026 0.002 PHE A 344 TRP 0.024 0.002 TRP E 400 HIS 0.006 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (10552) covalent geometry : angle 0.70714 / 0.39 (14758) hydrogen bonds : bond 0.09903 / 6.73 ( 521) hydrogen bonds : angle 5.30959 / 3.63 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.216 Fit side-chains REVERT: E 36 LEU cc_start: 0.7775 (mm) cc_final: 0.7432 (mm) REVERT: E 38 LEU cc_start: 0.9257 (mt) cc_final: 0.8859 (mm) REVERT: E 119 ILE cc_start: 0.8881 (pt) cc_final: 0.8527 (mm) REVERT: E 173 MET cc_start: 0.8499 (mtp) cc_final: 0.8215 (ttm) REVERT: E 250 MET cc_start: 0.8673 (ttm) cc_final: 0.7972 (ttm) REVERT: E 337 ASP cc_start: 0.7700 (p0) cc_final: 0.6360 (t0) REVERT: E 344 PHE cc_start: 0.8733 (t80) cc_final: 0.8223 (t80) REVERT: E 351 THR cc_start: 0.8432 (t) cc_final: 0.7869 (t) REVERT: E 370 GLN cc_start: 0.8610 (mt0) cc_final: 0.8374 (mt0) REVERT: E 394 TYR cc_start: 0.7638 (t80) cc_final: 0.7383 (t80) REVERT: E 403 MET cc_start: 0.8009 (pmm) cc_final: 0.7319 (pmm) REVERT: E 492 THR cc_start: 0.8874 (m) cc_final: 0.8577 (m) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0668 time to fit residues: 6.4996 Evaluate side-chains 49 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.155 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0056 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079365 restraints weight = 14442.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081502 restraints weight = 8731.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082861 restraints weight = 5805.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084076 restraints weight = 4248.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084919 restraints weight = 3226.178| |-----------------------------------------------------------------------------| r_work (final): 0.3363 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.111562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103273 restraints weight = 3273.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.104437 restraints weight = 1620.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.105141 restraints weight = 1150.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.105144 restraints weight = 971.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.105248 restraints weight = 969.730| |-----------------------------------------------------------------------------| r_work (final): 0.3821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073735 restraints weight = 2674.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074983 restraints weight = 1193.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075635 restraints weight = 616.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076102 restraints weight = 371.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076300 restraints weight = 229.248| |-----------------------------------------------------------------------------| r_work (final): 0.3236 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.094016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.087185 restraints weight = 6809.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087898 restraints weight = 2628.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088245 restraints weight = 1765.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088287 restraints weight = 1542.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088287 restraints weight = 1506.931| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10552 Z= 0.178 Angle : 0.735 11.091 14758 Z= 0.401 Chirality : 0.044 0.170 1674 Planarity : 0.005 0.045 1450 Dihedral : 27.659 89.620 2342 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.60 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -1.06 (0.26), residues: 956 helix: 0.04 (0.23), residues: 498 sheet: -0.57 (0.60), residues: 62 loop : -1.64 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 364 TYR 0.014 0.001 TYR A 488 PHE 0.025 0.002 PHE A 317 TRP 0.014 0.002 TRP A 122 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (10552) covalent geometry : angle 0.73462 / 0.40 (14758) hydrogen bonds : bond 0.09999 / 6.74 ( 521) hydrogen bonds : angle 5.27399 / 3.61 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.122 Fit side-chains REVERT: E 36 LEU cc_start: 0.7795 (mm) cc_final: 0.7448 (mm) REVERT: E 38 LEU cc_start: 0.9229 (mt) cc_final: 0.8825 (mm) REVERT: E 119 ILE cc_start: 0.8670 (pt) cc_final: 0.8325 (mm) REVERT: E 120 SER cc_start: 0.8506 (p) cc_final: 0.8091 (m) REVERT: E 173 MET cc_start: 0.8698 (mtp) cc_final: 0.8384 (ttm) REVERT: E 250 MET cc_start: 0.8640 (ttm) cc_final: 0.7964 (ttm) REVERT: E 337 ASP cc_start: 0.7728 (p0) cc_final: 0.6314 (t0) REVERT: E 344 PHE cc_start: 0.8795 (t80) cc_final: 0.8481 (t80) REVERT: E 370 GLN cc_start: 0.8682 (mt0) cc_final: 0.8370 (mt0) REVERT: E 403 MET cc_start: 0.7974 (pmm) cc_final: 0.7167 (pmm) REVERT: E 492 THR cc_start: 0.8868 (m) cc_final: 0.8579 (m) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0479 time to fit residues: 4.5397 Evaluate side-chains 49 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.139 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0047 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0053 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0101 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.0050 chunk 11 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 0.0570 chunk 94 optimal weight: 4.9990 overall best weight: 1.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079084 restraints weight = 14798.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081199 restraints weight = 8876.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082726 restraints weight = 5893.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083819 restraints weight = 4228.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084503 restraints weight = 3222.943| |-----------------------------------------------------------------------------| r_work (final): 0.3353 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.111772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.103572 restraints weight = 3222.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104047 restraints weight = 1615.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105266 restraints weight = 1278.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.105327 restraints weight = 1018.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.105327 restraints weight = 992.574| |-----------------------------------------------------------------------------| r_work (final): 0.3829 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074481 restraints weight = 2782.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.075773 restraints weight = 1208.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076522 restraints weight = 638.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076921 restraints weight = 369.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077111 restraints weight = 228.023| |-----------------------------------------------------------------------------| r_work (final): 0.3252 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.091777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087292 restraints weight = 6868.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087950 restraints weight = 2816.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088438 restraints weight = 1787.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088438 restraints weight = 1388.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088438 restraints weight = 1388.270| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10552 Z= 0.143 Angle : 0.718 18.000 14758 Z= 0.386 Chirality : 0.043 0.183 1674 Planarity : 0.004 0.040 1450 Dihedral : 27.554 82.629 2342 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.39 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: -0.95 (0.26), residues: 956 helix: 0.16 (0.23), residues: 520 sheet: -0.94 (0.60), residues: 64 loop : -1.64 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 437 TYR 0.017 0.002 TYR A 394 PHE 0.023 0.002 PHE A 317 TRP 0.006 0.001 TRP E 41 HIS 0.006 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (10552) covalent geometry : angle 0.71817 / 0.39 (14758) hydrogen bonds : bond 0.09827 / 6.68 ( 521) hydrogen bonds : angle 5.21629 / 3.56 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.144 Fit side-chains REVERT: E 36 LEU cc_start: 0.7866 (mm) cc_final: 0.7581 (mm) REVERT: E 119 ILE cc_start: 0.8673 (pt) cc_final: 0.8314 (mm) REVERT: E 120 SER cc_start: 0.8628 (p) cc_final: 0.8161 (m) REVERT: E 173 MET cc_start: 0.9007 (mtp) cc_final: 0.8705 (ttm) REVERT: E 250 MET cc_start: 0.8621 (ttm) cc_final: 0.8006 (ttm) REVERT: E 315 ASP cc_start: 0.8581 (m-30) cc_final: 0.6975 (p0) REVERT: E 337 ASP cc_start: 0.7758 (p0) cc_final: 0.6297 (t0) REVERT: E 351 THR cc_start: 0.8342 (t) cc_final: 0.7801 (t) REVERT: E 370 GLN cc_start: 0.8720 (mt0) cc_final: 0.8407 (mt0) REVERT: E 403 MET cc_start: 0.7874 (pmm) cc_final: 0.7068 (pmm) REVERT: E 492 THR cc_start: 0.8882 (m) cc_final: 0.8247 (m) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0552 time to fit residues: 5.3336 Evaluate side-chains 49 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.148 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0055 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0097 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078887 restraints weight = 14720.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080959 restraints weight = 9063.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082259 restraints weight = 6136.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083507 restraints weight = 4565.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084288 restraints weight = 3504.327| |-----------------------------------------------------------------------------| r_work (final): 0.3341 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.111436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103198 restraints weight = 3215.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104192 restraints weight = 1667.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104954 restraints weight = 1216.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.105300 restraints weight = 991.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.105300 restraints weight = 920.702| |-----------------------------------------------------------------------------| r_work (final): 0.3820 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074592 restraints weight = 2724.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075858 restraints weight = 1174.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076563 restraints weight = 614.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076978 restraints weight = 347.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077163 restraints weight = 216.333| |-----------------------------------------------------------------------------| r_work (final): 0.3255 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088705 restraints weight = 6543.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089244 restraints weight = 2817.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089680 restraints weight = 1915.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089691 restraints weight = 1516.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089691 restraints weight = 1501.060| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10552 Z= 0.155 Angle : 0.701 12.598 14758 Z= 0.386 Chirality : 0.042 0.172 1674 Planarity : 0.004 0.039 1450 Dihedral : 27.518 84.282 2342 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -0.83 (0.26), residues: 956 helix: 0.26 (0.23), residues: 508 sheet: -1.01 (0.59), residues: 64 loop : -1.53 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 437 TYR 0.014 0.001 TYR A 398 PHE 0.036 0.002 PHE A 344 TRP 0.008 0.001 TRP E 122 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (10552) covalent geometry : angle 0.70066 / 0.39 (14758) hydrogen bonds : bond 0.09786 / 6.67 ( 521) hydrogen bonds : angle 5.18849 / 3.55 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7932 (mm) cc_final: 0.7622 (mm) REVERT: E 120 SER cc_start: 0.8757 (p) cc_final: 0.8397 (m) REVERT: E 173 MET cc_start: 0.8799 (mtp) cc_final: 0.8530 (ttm) REVERT: E 250 MET cc_start: 0.8661 (ttm) cc_final: 0.7897 (ttm) REVERT: E 337 ASP cc_start: 0.7943 (p0) cc_final: 0.6423 (t0) REVERT: E 370 GLN cc_start: 0.8698 (mt0) cc_final: 0.8064 (mm-40) REVERT: E 403 MET cc_start: 0.7911 (pmm) cc_final: 0.7091 (pmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0458 time to fit residues: 4.3835 Evaluate side-chains 50 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.157 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0048 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0053 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 0.0770 chunk 71 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.081328 restraints weight = 15052.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083472 restraints weight = 9282.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084987 restraints weight = 6290.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086087 restraints weight = 4577.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086968 restraints weight = 3547.220| |-----------------------------------------------------------------------------| r_work (final): 0.3388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.113395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105480 restraints weight = 3078.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106554 restraints weight = 1621.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107192 restraints weight = 1178.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107629 restraints weight = 974.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107629 restraints weight = 897.609| |-----------------------------------------------------------------------------| r_work (final): 0.3868 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076310 restraints weight = 2680.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077584 restraints weight = 1188.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078279 restraints weight = 605.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078652 restraints weight = 360.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078887 restraints weight = 241.657| |-----------------------------------------------------------------------------| r_work (final): 0.3286 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.097390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085632 restraints weight = 5718.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.086607 restraints weight = 2625.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.087278 restraints weight = 1813.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087645 restraints weight = 1489.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.087687 restraints weight = 1363.946| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10552 Z= 0.138 Angle : 0.709 9.660 14758 Z= 0.384 Chirality : 0.043 0.170 1674 Planarity : 0.005 0.039 1450 Dihedral : 27.405 82.515 2342 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.39 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -0.72 (0.27), residues: 956 helix: 0.38 (0.24), residues: 496 sheet: -1.13 (0.54), residues: 62 loop : -1.41 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 437 TYR 0.018 0.002 TYR E 394 PHE 0.038 0.002 PHE A 317 TRP 0.012 0.001 TRP E 122 HIS 0.008 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (10552) covalent geometry : angle 0.70934 / 0.38 (14758) hydrogen bonds : bond 0.09788 / 6.73 ( 521) hydrogen bonds : angle 5.06293 / 3.47 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7901 (mm) cc_final: 0.7627 (mm) REVERT: E 83 ASP cc_start: 0.7736 (m-30) cc_final: 0.7509 (m-30) REVERT: E 173 MET cc_start: 0.8747 (mtp) cc_final: 0.8289 (ttm) REVERT: E 250 MET cc_start: 0.8660 (ttm) cc_final: 0.7832 (ttm) REVERT: E 323 LEU cc_start: 0.6614 (pt) cc_final: 0.4931 (mt) REVERT: E 337 ASP cc_start: 0.7839 (p0) cc_final: 0.6448 (t0) REVERT: E 370 GLN cc_start: 0.8742 (mt0) cc_final: 0.8036 (mm-40) REVERT: E 403 MET cc_start: 0.7877 (pmm) cc_final: 0.7086 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0541 time to fit residues: 5.2536 Evaluate side-chains 54 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.154 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0049 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0055 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0093 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 95 optimal weight: 0.0970 chunk 50 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080601 restraints weight = 14951.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082667 restraints weight = 9307.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084185 restraints weight = 6345.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085092 restraints weight = 4631.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086078 restraints weight = 3662.737| |-----------------------------------------------------------------------------| r_work (final): 0.3368 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.112660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.104744 restraints weight = 3045.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105292 restraints weight = 1601.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.106279 restraints weight = 1256.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.106423 restraints weight = 1038.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.106423 restraints weight = 978.817| |-----------------------------------------------------------------------------| r_work (final): 0.3837 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.077332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074808 restraints weight = 2809.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.075655 restraints weight = 905.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076178 restraints weight = 421.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076493 restraints weight = 247.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076636 restraints weight = 158.781| |-----------------------------------------------------------------------------| r_work (final): 0.3260 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089985 restraints weight = 6387.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090534 restraints weight = 2771.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090952 restraints weight = 1858.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090952 restraints weight = 1499.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090952 restraints weight = 1499.501| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10552 Z= 0.139 Angle : 0.684 11.225 14758 Z= 0.375 Chirality : 0.041 0.169 1674 Planarity : 0.004 0.040 1450 Dihedral : 27.282 80.240 2342 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.39 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.59 (0.27), residues: 956 helix: 0.42 (0.23), residues: 508 sheet: -1.24 (0.59), residues: 62 loop : -1.27 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 437 TYR 0.015 0.001 TYR A 398 PHE 0.026 0.002 PHE A 317 TRP 0.010 0.002 TRP A 122 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (10552) covalent geometry : angle 0.68380 / 0.38 (14758) hydrogen bonds : bond 0.09662 / 6.58 ( 521) hydrogen bonds : angle 5.08039 / 3.48 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7945 (mm) cc_final: 0.7744 (mm) REVERT: E 83 ASP cc_start: 0.7789 (m-30) cc_final: 0.7544 (m-30) REVERT: E 173 MET cc_start: 0.8774 (mtp) cc_final: 0.8471 (ttm) REVERT: E 187 LYS cc_start: 0.7540 (ptpp) cc_final: 0.6443 (tmtt) REVERT: E 250 MET cc_start: 0.8731 (ttm) cc_final: 0.7939 (ttm) REVERT: E 337 ASP cc_start: 0.8012 (p0) cc_final: 0.6428 (t0) REVERT: E 370 GLN cc_start: 0.8735 (mt0) cc_final: 0.8050 (mm-40) REVERT: E 403 MET cc_start: 0.7828 (pmm) cc_final: 0.6903 (pmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0643 time to fit residues: 5.3894 Evaluate side-chains 46 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.152 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0055 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0088 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 97 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078790 restraints weight = 15221.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080783 restraints weight = 9447.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082214 restraints weight = 6421.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.083213 restraints weight = 4717.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083885 restraints weight = 3677.191| |-----------------------------------------------------------------------------| r_work (final): 0.3328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.110608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102511 restraints weight = 2954.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.103575 restraints weight = 1605.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.104229 restraints weight = 1179.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.104354 restraints weight = 1007.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.104354 restraints weight = 959.512| |-----------------------------------------------------------------------------| r_work (final): 0.3819 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075256 restraints weight = 2801.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076004 restraints weight = 843.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076507 restraints weight = 386.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.076839 restraints weight = 225.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076925 restraints weight = 146.132| |-----------------------------------------------------------------------------| r_work (final): 0.3253 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.096891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084657 restraints weight = 5958.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085681 restraints weight = 2714.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086201 restraints weight = 1826.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086610 restraints weight = 1535.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086610 restraints weight = 1397.710| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10552 Z= 0.172 Angle : 0.700 9.394 14758 Z= 0.384 Chirality : 0.042 0.173 1674 Planarity : 0.005 0.039 1450 Dihedral : 27.211 79.972 2342 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.65 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.62 (0.27), residues: 956 helix: 0.34 (0.23), residues: 508 sheet: -1.27 (0.56), residues: 70 loop : -1.17 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 437 TYR 0.011 0.002 TYR A 394 PHE 0.026 0.002 PHE A 317 TRP 0.012 0.002 TRP A 122 HIS 0.006 0.002 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (10552) covalent geometry : angle 0.69970 / 0.38 (14758) hydrogen bonds : bond 0.09694 / 6.56 ( 521) hydrogen bonds : angle 5.18316 / 3.55 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7801 (m-30) cc_final: 0.7560 (m-30) REVERT: E 173 MET cc_start: 0.8794 (mtp) cc_final: 0.8518 (ttm) REVERT: E 250 MET cc_start: 0.8728 (ttm) cc_final: 0.7887 (ttm) REVERT: E 337 ASP cc_start: 0.8053 (p0) cc_final: 0.6357 (t0) REVERT: E 370 GLN cc_start: 0.8745 (mt0) cc_final: 0.8532 (mt0) REVERT: E 403 MET cc_start: 0.7762 (pmm) cc_final: 0.6761 (pmm) REVERT: E 492 THR cc_start: 0.9043 (m) cc_final: 0.8459 (m) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0493 time to fit residues: 4.1197 Evaluate side-chains 40 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0049 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0053 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0099 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 40.0000 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079849 restraints weight = 15518.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081865 restraints weight = 9622.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083300 restraints weight = 6581.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084302 restraints weight = 4843.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085116 restraints weight = 3783.145| |-----------------------------------------------------------------------------| r_work (final): 0.3349 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.111889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.103748 restraints weight = 3212.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104526 restraints weight = 1668.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.105347 restraints weight = 1244.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.105564 restraints weight = 1061.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.105564 restraints weight = 963.406| |-----------------------------------------------------------------------------| r_work (final): 0.3855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.075129 restraints weight = 2944.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075890 restraints weight = 868.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076364 restraints weight = 393.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.076550 restraints weight = 223.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.076549 restraints weight = 180.853| |-----------------------------------------------------------------------------| r_work (final): 0.3234 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.091292 restraints weight = 6093.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091878 restraints weight = 2599.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092083 restraints weight = 1771.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092094 restraints weight = 1577.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092103 restraints weight = 1560.988| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10552 Z= 0.144 Angle : 0.669 8.088 14758 Z= 0.370 Chirality : 0.041 0.173 1674 Planarity : 0.004 0.040 1450 Dihedral : 27.163 80.650 2342 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.27), residues: 956 helix: 0.35 (0.23), residues: 508 sheet: -1.37 (0.55), residues: 70 loop : -1.14 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 437 TYR 0.010 0.001 TYR A 398 PHE 0.027 0.002 PHE E 317 TRP 0.014 0.002 TRP A 122 HIS 0.006 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (10552) covalent geometry : angle 0.66916 / 0.37 (14758) hydrogen bonds : bond 0.09547 / 6.50 ( 521) hydrogen bonds : angle 5.09437 / 3.49 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.80 seconds wall clock time: 19 minutes 58.67 seconds (1198.67 seconds total)