Starting phenix.real_space_refine on Tue Nov 18 01:34:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqx_20455/11_2025/6pqx_20455.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqx_20455/11_2025/6pqx_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pqx_20455/11_2025/6pqx_20455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqx_20455/11_2025/6pqx_20455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqx_20455/11_2025/6pqx_20455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqx_20455/11_2025/6pqx_20455.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 2.51, per 1000 atoms: 0.25 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: 1.01 Conformation dependent library (CDL) restraints added in 269.9 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: 1.46 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: 1.88 Time building geometry restraints manager: 1.31 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=" O3' DA H 19 " pdb=" P DT H 20 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.20e+01 bond pdb=" O3' DC D 5 " pdb=" P DG D 6 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.19e+01 bond pdb=" O3' DA H 11 " pdb=" P DC H 12 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.11e+01 bond pdb=" O3' DA D 11 " pdb=" P DC D 12 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.50e-02 4.44e+03 7.56e+00 bond pdb=" O3' DA D 19 " pdb=" P DT D 20 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.88e+00 ... (remaining 10547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 13995 2.05 - 4.10: 646 4.10 - 6.16: 102 6.16 - 8.21: 12 8.21 - 10.26: 3 Bond angle restraints: 14758 Sorted by residual: angle pdb=" O3' DC H 5 " pdb=" C3' DC H 5 " pdb=" C2' DC H 5 " ideal model delta sigma weight residual 111.50 121.76 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C4' DG H 18 " pdb=" C3' DG H 18 " pdb=" O3' DG H 18 " ideal model delta sigma weight residual 110.00 103.09 6.91 1.50e+00 4.44e-01 2.12e+01 angle pdb=" O3' DG D 29 " pdb=" C3' DG D 29 " pdb=" C2' DG D 29 " ideal model delta sigma weight residual 111.50 104.61 6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" C4' DG D 18 " pdb=" C3' DG D 18 " pdb=" O3' DG D 18 " ideal model delta sigma weight residual 110.00 103.16 6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" O3' DG H 29 " pdb=" C3' DG H 29 " pdb=" C2' DG H 29 " ideal model delta sigma weight residual 111.50 104.71 6.79 1.50e+00 4.44e-01 2.05e+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 - 0.068: 1333 0.068 - 0.136: 301 0.136 - 0.204: 33 0.204 - 0.273: 4 0.273 - 0.341: 3 Chirality restraints: 1674 Sorted by residual: 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 -0.34 2.00e-01 2.50e+01 2.90e+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 -0.34 2.00e-01 2.50e+01 2.89e+00 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 -2.66 -2.36 -0.30 2.00e-01 2.50e+01 2.31e+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: 0.650 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10552 Z= 0.296 Angle : 0.988 10.262 14758 Z= 0.601 Chirality : 0.058 0.341 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 covalent geometry : bond 0.00605 (10552) covalent geometry : angle 0.98829 (14758) hydrogen bonds : bond 0.16704 ( 521) hydrogen bonds : angle 7.21869 ( 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 : 0.145 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: 0.6848 (p) REVERT: A 169 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8107 (Cg_endo) REVERT: A 201 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9005 (tt) REVERT: A 220 MET cc_start: 0.7638 (tmm) cc_final: 0.6958 (tmm) REVERT: A 250 MET cc_start: 0.8661 (ttm) cc_final: 0.7667 (ttm) REVERT: A 344 PHE cc_start: 0.8858 (t80) cc_final: 0.8497 (t80) REVERT: A 364 ARG cc_start: 0.8467 (mtp85) cc_final: 0.7944 (mtp180) REVERT: A 403 MET cc_start: 0.7867 (pmm) cc_final: 0.6992 (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: 0.0891 time to fit residues: 10.4738 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 : 0.163 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 : 0.003 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: 0.0055 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 7.9990 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: E 136 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078023 restraints weight = 15486.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080079 restraints weight = 9792.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081486 restraints weight = 6749.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082625 restraints weight = 4994.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083471 restraints weight = 3864.003| |-----------------------------------------------------------------------------| r_work (final): 0.3320 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.111241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.109772 restraints weight = 3155.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.110377 restraints weight = 1135.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110641 restraints weight = 485.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110641 restraints weight = 310.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110641 restraints weight = 310.270| |-----------------------------------------------------------------------------| r_work (final): 0.3939 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071432 restraints weight = 2839.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072617 restraints weight = 1247.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073353 restraints weight = 668.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073838 restraints weight = 395.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.074072 restraints weight = 256.276| |-----------------------------------------------------------------------------| r_work (final): 0.3189 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.091978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085190 restraints weight = 6296.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085796 restraints weight = 2249.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085796 restraints weight = 1706.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085796 restraints weight = 1706.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085796 restraints weight = 1706.594| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10552 Z= 0.175 Angle : 0.712 9.581 14758 Z= 0.393 Chirality : 0.040 0.140 1674 Planarity : 0.005 0.048 1450 Dihedral : 27.633 84.762 2342 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: -1.72 (0.25), residues: 956 helix: -0.48 (0.22), residues: 498 sheet: -0.83 (0.72), residues: 48 loop : -1.96 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 485 TYR 0.008 0.001 TYR A 266 PHE 0.017 0.002 PHE A 344 TRP 0.018 0.002 TRP E 41 HIS 0.007 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00383 (10552) covalent geometry : angle 0.71216 (14758) hydrogen bonds : bond 0.09750 ( 521) hydrogen bonds : angle 5.55871 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: E 119 ILE cc_start: 0.8905 (pt) cc_final: 0.8585 (mm) REVERT: E 250 MET cc_start: 0.8693 (ttm) cc_final: 0.7900 (ttm) REVERT: E 282 CYS cc_start: 0.8629 (p) cc_final: 0.8393 (p) REVERT: E 370 GLN cc_start: 0.8724 (mt0) cc_final: 0.8379 (mt0) REVERT: E 403 MET cc_start: 0.8042 (pmm) cc_final: 0.7343 (pmm) REVERT: E 439 LYS cc_start: 0.8192 (tttt) cc_final: 0.7982 (tptt) REVERT: E 492 THR cc_start: 0.9066 (m) cc_final: 0.8826 (m) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0960 time to fit residues: 9.1652 Evaluate side-chains 44 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.153 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: 0.0054 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 : 0.004 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: 0.0096 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 105 optimal weight: 0.0030 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 9 optimal weight: 0.0020 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077474 restraints weight = 15279.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079541 restraints weight = 9434.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080895 restraints weight = 6393.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082033 restraints weight = 4706.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082757 restraints weight = 3636.376| |-----------------------------------------------------------------------------| r_work (final): 0.3315 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.110082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.102519 restraints weight = 2934.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.103504 restraints weight = 1573.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.104026 restraints weight = 1146.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.104086 restraints weight = 1030.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.104086 restraints weight = 1002.552| |-----------------------------------------------------------------------------| r_work (final): 0.3821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072032 restraints weight = 2876.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073266 restraints weight = 1269.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.073952 restraints weight = 664.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074298 restraints weight = 385.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074596 restraints weight = 262.465| |-----------------------------------------------------------------------------| r_work (final): 0.3214 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.093775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.084122 restraints weight = 5749.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083499 restraints weight = 4403.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084004 restraints weight = 2961.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083890 restraints weight = 2466.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083938 restraints weight = 2181.876| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10552 Z= 0.184 Angle : 0.670 7.457 14758 Z= 0.377 Chirality : 0.039 0.135 1674 Planarity : 0.005 0.061 1450 Dihedral : 27.381 82.853 2342 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.86 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -1.52 (0.26), residues: 956 helix: -0.37 (0.22), residues: 510 sheet: -0.80 (0.64), residues: 62 loop : -1.83 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 485 TYR 0.009 0.001 TYR E 488 PHE 0.023 0.002 PHE A 317 TRP 0.011 0.002 TRP E 41 HIS 0.007 0.002 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00395 (10552) covalent geometry : angle 0.67029 (14758) hydrogen bonds : bond 0.09599 ( 521) hydrogen bonds : angle 5.29615 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 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 : 0.167 Fit side-chains REVERT: E 119 ILE cc_start: 0.8876 (pt) cc_final: 0.8500 (mm) REVERT: E 250 MET cc_start: 0.8656 (ttm) cc_final: 0.8035 (ttm) REVERT: E 337 ASP cc_start: 0.7803 (p0) cc_final: 0.6408 (t0) REVERT: E 370 GLN cc_start: 0.8570 (mt0) cc_final: 0.8000 (mm-40) REVERT: E 394 TYR cc_start: 0.7708 (t80) cc_final: 0.7431 (t80) REVERT: E 403 MET cc_start: 0.7989 (pmm) cc_final: 0.7170 (pmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0796 time to fit residues: 6.9023 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 : 0.155 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: 0.0047 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: 0.0054 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 : 0.004 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: 0.0095 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: 3.9990 chunk 99 optimal weight: 0.0050 chunk 38 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 0.0050 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.7612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080059 restraints weight = 15002.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082143 restraints weight = 9230.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083569 restraints weight = 6234.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084667 restraints weight = 4552.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085497 restraints weight = 3500.058| |-----------------------------------------------------------------------------| r_work (final): 0.3362 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.111029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.103751 restraints weight = 3035.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.104970 restraints weight = 1506.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.105689 restraints weight = 1041.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.106098 restraints weight = 870.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106182 restraints weight = 787.064| |-----------------------------------------------------------------------------| r_work (final): 0.3870 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073722 restraints weight = 2704.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074893 restraints weight = 1153.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075430 restraints weight = 595.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075874 restraints weight = 370.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076040 restraints weight = 237.866| |-----------------------------------------------------------------------------| r_work (final): 0.3245 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088413 restraints weight = 6072.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089085 restraints weight = 2518.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089424 restraints weight = 1770.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089424 restraints weight = 1560.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089424 restraints weight = 1560.595| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10552 Z= 0.153 Angle : 0.655 7.340 14758 Z= 0.366 Chirality : 0.038 0.173 1674 Planarity : 0.005 0.042 1450 Dihedral : 27.352 88.974 2342 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.44 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.26), residues: 956 helix: -0.25 (0.23), residues: 510 sheet: -0.90 (0.60), residues: 64 loop : -1.96 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 442 TYR 0.007 0.001 TYR E 59 PHE 0.024 0.002 PHE E 317 TRP 0.018 0.002 TRP E 400 HIS 0.008 0.002 HIS E 447 Details of bonding type rmsd covalent geometry : bond 0.00329 (10552) covalent geometry : angle 0.65516 (14758) hydrogen bonds : bond 0.09567 ( 521) hydrogen bonds : angle 5.14968 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 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 : 0.155 Fit side-chains REVERT: E 38 LEU cc_start: 0.9252 (mt) cc_final: 0.8791 (mm) REVERT: E 250 MET cc_start: 0.8584 (ttm) cc_final: 0.7971 (ttm) REVERT: E 315 ASP cc_start: 0.8540 (m-30) cc_final: 0.8333 (m-30) REVERT: E 370 GLN cc_start: 0.8659 (mt0) cc_final: 0.8456 (mt0) REVERT: E 394 TYR cc_start: 0.7553 (t80) cc_final: 0.7285 (t80) REVERT: E 403 MET cc_start: 0.7955 (pmm) cc_final: 0.7262 (pmm) REVERT: E 492 THR cc_start: 0.8873 (m) cc_final: 0.8293 (m) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0685 time to fit residues: 6.2662 Evaluate side-chains 43 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.164 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: 0.0056 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: 0.0094 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 90 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082580 restraints weight = 14702.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084742 restraints weight = 9020.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086250 restraints weight = 6066.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087400 restraints weight = 4388.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088243 restraints weight = 3342.117| |-----------------------------------------------------------------------------| r_work (final): 0.3419 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.112832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.105302 restraints weight = 3101.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.106375 restraints weight = 1600.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106668 restraints weight = 1133.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106730 restraints weight = 1010.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106745 restraints weight = 983.343| |-----------------------------------------------------------------------------| r_work (final): 0.3881 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075997 restraints weight = 2759.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077132 restraints weight = 1156.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077790 restraints weight = 574.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078148 restraints weight = 327.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078326 restraints weight = 206.428| |-----------------------------------------------------------------------------| r_work (final): 0.3288 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089993 restraints weight = 6991.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090545 restraints weight = 2733.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090546 restraints weight = 1830.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090546 restraints weight = 1828.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090546 restraints weight = 1828.617| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10552 Z= 0.136 Angle : 0.630 7.257 14758 Z= 0.348 Chirality : 0.037 0.135 1674 Planarity : 0.004 0.042 1450 Dihedral : 27.195 81.897 2342 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.07 % Favored : 93.72 % 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: -1.45 (0.26), residues: 956 helix: -0.18 (0.23), residues: 508 sheet: -1.17 (0.59), residues: 64 loop : -1.92 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 445 TYR 0.008 0.001 TYR E 62 PHE 0.022 0.001 PHE E 317 TRP 0.009 0.001 TRP E 400 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00288 (10552) covalent geometry : angle 0.62954 (14758) hydrogen bonds : bond 0.09522 ( 521) hydrogen bonds : angle 5.01222 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 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 : 0.143 Fit side-chains REVERT: E 83 ASP cc_start: 0.7788 (m-30) cc_final: 0.7478 (m-30) REVERT: E 122 TRP cc_start: 0.8746 (p-90) cc_final: 0.7350 (p-90) REVERT: E 220 MET cc_start: 0.8443 (tpt) cc_final: 0.7848 (tpt) REVERT: E 250 MET cc_start: 0.8616 (ttm) cc_final: 0.7923 (ttm) REVERT: E 323 LEU cc_start: 0.6603 (pt) cc_final: 0.5106 (mt) REVERT: E 337 ASP cc_start: 0.7754 (p0) cc_final: 0.6324 (t0) REVERT: E 370 GLN cc_start: 0.8708 (mt0) cc_final: 0.8043 (tp40) REVERT: E 403 MET cc_start: 0.7993 (pmm) cc_final: 0.7172 (pmm) REVERT: E 431 GLU cc_start: 0.7136 (pt0) cc_final: 0.6838 (pt0) REVERT: E 462 LEU cc_start: 0.8939 (tt) cc_final: 0.8629 (mt) REVERT: E 464 MET cc_start: 0.8988 (tpp) cc_final: 0.8773 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0666 time to fit residues: 6.2873 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 : 0.152 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: 0.0047 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 : 0.003 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: 0.0054 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 : 0.004 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: 0.0090 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: 0.1980 chunk 11 optimal weight: 0.0470 chunk 92 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 68 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081174 restraints weight = 14614.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083381 restraints weight = 8954.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085000 restraints weight = 6049.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086156 restraints weight = 4387.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087041 restraints weight = 3366.180| |-----------------------------------------------------------------------------| r_work (final): 0.3403 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.113787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.105929 restraints weight = 3108.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.106455 restraints weight = 1596.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107569 restraints weight = 1253.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107570 restraints weight = 1008.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107570 restraints weight = 1008.696| |-----------------------------------------------------------------------------| r_work (final): 0.3882 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075055 restraints weight = 2884.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075974 restraints weight = 841.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076560 restraints weight = 375.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076850 restraints weight = 204.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076850 restraints weight = 145.326| |-----------------------------------------------------------------------------| r_work (final): 0.3255 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086618 restraints weight = 5760.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087482 restraints weight = 2709.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.088278 restraints weight = 1840.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088559 restraints weight = 1467.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088559 restraints weight = 1355.175| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4130 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= 0.136 Angle : 0.619 11.748 14758 Z= 0.338 Chirality : 0.037 0.143 1674 Planarity : 0.005 0.058 1450 Dihedral : 27.052 81.381 2342 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -1.27 (0.26), residues: 956 helix: -0.10 (0.23), residues: 508 sheet: -0.88 (0.58), residues: 70 loop : -1.80 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 437 TYR 0.016 0.001 TYR A 394 PHE 0.015 0.001 PHE E 317 TRP 0.006 0.001 TRP E 41 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00290 (10552) covalent geometry : angle 0.61858 (14758) hydrogen bonds : bond 0.09367 ( 521) hydrogen bonds : angle 4.98576 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 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 : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7737 (m-30) cc_final: 0.7469 (m-30) REVERT: E 122 TRP cc_start: 0.8733 (p-90) cc_final: 0.8486 (p-90) REVERT: E 250 MET cc_start: 0.8712 (ttm) cc_final: 0.7952 (ttm) REVERT: E 277 ILE cc_start: 0.9356 (mm) cc_final: 0.9130 (mm) REVERT: E 323 LEU cc_start: 0.6737 (pt) cc_final: 0.5292 (mt) REVERT: E 337 ASP cc_start: 0.7919 (p0) cc_final: 0.6390 (t0) REVERT: E 370 GLN cc_start: 0.8687 (mt0) cc_final: 0.8105 (tp40) REVERT: E 403 MET cc_start: 0.7873 (pmm) cc_final: 0.7008 (pmm) REVERT: E 447 HIS cc_start: 0.7382 (m90) cc_final: 0.6973 (m90) REVERT: E 462 LEU cc_start: 0.8906 (tt) cc_final: 0.8592 (mt) REVERT: E 464 MET cc_start: 0.9037 (tpp) cc_final: 0.8725 (tpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0611 time to fit residues: 5.6417 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 : 0.206 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: 0.0084 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: 0.0051 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082382 restraints weight = 14505.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084669 restraints weight = 8731.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086315 restraints weight = 5807.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087488 restraints weight = 4156.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088151 restraints weight = 3146.405| |-----------------------------------------------------------------------------| r_work (final): 0.3418 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106856 restraints weight = 2929.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.108009 restraints weight = 1261.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.108391 restraints weight = 825.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.109360 restraints weight = 717.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109395 restraints weight = 560.194| |-----------------------------------------------------------------------------| r_work (final): 0.3886 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078638 restraints weight = 2749.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079844 restraints weight = 1220.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080436 restraints weight = 624.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080769 restraints weight = 373.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.080956 restraints weight = 247.320| |-----------------------------------------------------------------------------| r_work (final): 0.3335 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.098608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087094 restraints weight = 5578.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.087940 restraints weight = 2787.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088399 restraints weight = 1942.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088700 restraints weight = 1687.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088928 restraints weight = 1542.127| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10552 Z= 0.134 Angle : 0.605 7.258 14758 Z= 0.336 Chirality : 0.037 0.138 1674 Planarity : 0.004 0.035 1450 Dihedral : 26.925 81.157 2342 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.86 % Favored : 93.93 % 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: -1.34 (0.26), residues: 956 helix: -0.26 (0.22), residues: 508 sheet: -0.95 (0.56), residues: 70 loop : -1.65 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 443 TYR 0.006 0.001 TYR A 62 PHE 0.017 0.001 PHE A 317 TRP 0.008 0.001 TRP A 122 HIS 0.009 0.002 HIS E 447 Details of bonding type rmsd covalent geometry : bond 0.00285 (10552) covalent geometry : angle 0.60516 (14758) hydrogen bonds : bond 0.09312 ( 521) hydrogen bonds : angle 4.97565 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 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 : 0.146 Fit side-chains REVERT: E 83 ASP cc_start: 0.7732 (m-30) cc_final: 0.7468 (m-30) REVERT: E 122 TRP cc_start: 0.8559 (p-90) cc_final: 0.7835 (p-90) REVERT: E 173 MET cc_start: 0.8962 (mmm) cc_final: 0.8679 (tpp) REVERT: E 250 MET cc_start: 0.8707 (ttm) cc_final: 0.7924 (ttm) REVERT: E 277 ILE cc_start: 0.9357 (mm) cc_final: 0.9135 (mm) REVERT: E 323 LEU cc_start: 0.6752 (pt) cc_final: 0.5333 (mt) REVERT: E 337 ASP cc_start: 0.7945 (p0) cc_final: 0.6427 (t0) REVERT: E 370 GLN cc_start: 0.8706 (mt0) cc_final: 0.7963 (tm-30) REVERT: E 403 MET cc_start: 0.7900 (pmm) cc_final: 0.7004 (pmm) REVERT: E 461 ILE cc_start: 0.9028 (mm) cc_final: 0.8770 (mm) REVERT: E 462 LEU cc_start: 0.8889 (tt) cc_final: 0.8540 (mt) REVERT: E 464 MET cc_start: 0.9008 (tpp) cc_final: 0.8773 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0604 time to fit residues: 5.7832 Evaluate side-chains 45 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.145 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: 0.0047 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 : 0.003 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: 0.0052 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 : 0.007 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 : 0.007 ------------------------------------------------------------------------------- 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: 0.2980 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 0.0040 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 75 optimal weight: 0.0000 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082977 restraints weight = 14928.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085243 restraints weight = 9055.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086804 restraints weight = 6081.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087951 restraints weight = 4415.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088792 restraints weight = 3376.706| |-----------------------------------------------------------------------------| r_work (final): 0.3429 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.107237 restraints weight = 2936.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.108142 restraints weight = 1457.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.109032 restraints weight = 1079.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.109180 restraints weight = 863.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.109763 restraints weight = 820.021| |-----------------------------------------------------------------------------| r_work (final): 0.3877 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078630 restraints weight = 2643.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079569 restraints weight = 749.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.080063 restraints weight = 331.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080427 restraints weight = 203.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080650 restraints weight = 139.277| |-----------------------------------------------------------------------------| r_work (final): 0.3328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087921 restraints weight = 5717.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088906 restraints weight = 2478.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.089395 restraints weight = 1686.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.089433 restraints weight = 1449.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089786 restraints weight = 1411.217| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4621 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= 0.132 Angle : 0.609 7.698 14758 Z= 0.335 Chirality : 0.037 0.151 1674 Planarity : 0.004 0.034 1450 Dihedral : 26.784 79.239 2342 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.65 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -1.27 (0.26), residues: 956 helix: -0.21 (0.22), residues: 508 sheet: -1.12 (0.62), residues: 64 loop : -1.57 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.018 0.001 TYR A 394 PHE 0.017 0.001 PHE A 317 TRP 0.006 0.001 TRP A 41 HIS 0.005 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00284 (10552) covalent geometry : angle 0.60903 (14758) hydrogen bonds : bond 0.09326 ( 521) hydrogen bonds : angle 4.87671 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.156 Fit side-chains REVERT: E 122 TRP cc_start: 0.8255 (p-90) cc_final: 0.7522 (p-90) REVERT: E 220 MET cc_start: 0.8368 (tpt) cc_final: 0.7503 (tpt) REVERT: E 250 MET cc_start: 0.8658 (ttm) cc_final: 0.7889 (ttm) REVERT: E 277 ILE cc_start: 0.9362 (mm) cc_final: 0.9135 (mm) REVERT: E 323 LEU cc_start: 0.6649 (pt) cc_final: 0.5203 (mt) REVERT: E 337 ASP cc_start: 0.7905 (p0) cc_final: 0.6435 (t0) REVERT: E 370 GLN cc_start: 0.8731 (mt0) cc_final: 0.8036 (tp40) REVERT: E 403 MET cc_start: 0.7833 (pmm) cc_final: 0.6934 (pmm) REVERT: E 462 LEU cc_start: 0.8913 (tt) cc_final: 0.8622 (mt) REVERT: E 464 MET cc_start: 0.8975 (tpp) cc_final: 0.8648 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0562 time to fit residues: 5.3250 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 : 0.158 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 : 0.004 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 : 0.004 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 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: 5.9990 chunk 46 optimal weight: 0.0020 chunk 103 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 52 optimal weight: 6.9990 overall best weight: 2.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081928 restraints weight = 15019.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084018 restraints weight = 9282.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.085511 restraints weight = 6322.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086605 restraints weight = 4627.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087336 restraints weight = 3553.436| |-----------------------------------------------------------------------------| r_work (final): 0.3397 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.112472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.105151 restraints weight = 2890.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.106104 restraints weight = 1272.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.106839 restraints weight = 883.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.106839 restraints weight = 703.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.106839 restraints weight = 703.504| |-----------------------------------------------------------------------------| r_work (final): 0.3845 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077609 restraints weight = 2727.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078440 restraints weight = 745.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078899 restraints weight = 322.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079265 restraints weight = 197.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079349 restraints weight = 124.392| |-----------------------------------------------------------------------------| r_work (final): 0.3352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085075 restraints weight = 5669.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085932 restraints weight = 2285.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086469 restraints weight = 1613.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086564 restraints weight = 1395.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086564 restraints weight = 1347.310| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10552 Z= 0.153 Angle : 0.603 7.350 14758 Z= 0.338 Chirality : 0.037 0.139 1674 Planarity : 0.004 0.036 1450 Dihedral : 26.720 79.996 2342 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.07 % Favored : 93.72 % 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: -1.20 (0.26), residues: 956 helix: -0.17 (0.23), residues: 508 sheet: -1.00 (0.58), residues: 70 loop : -1.51 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.016 0.001 TYR A 488 PHE 0.016 0.001 PHE A 317 TRP 0.005 0.001 TRP A 41 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00328 (10552) covalent geometry : angle 0.60334 (14758) hydrogen bonds : bond 0.09359 ( 521) hydrogen bonds : angle 4.90660 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7777 (m-30) cc_final: 0.7440 (m-30) REVERT: E 122 TRP cc_start: 0.8719 (p-90) cc_final: 0.7623 (p-90) REVERT: E 220 MET cc_start: 0.8461 (tpt) cc_final: 0.7576 (tpt) REVERT: E 250 MET cc_start: 0.8597 (ttm) cc_final: 0.7847 (ttm) REVERT: E 277 ILE cc_start: 0.9377 (mm) cc_final: 0.9143 (mm) REVERT: E 323 LEU cc_start: 0.6831 (pt) cc_final: 0.5358 (mt) REVERT: E 337 ASP cc_start: 0.8173 (p0) cc_final: 0.6492 (t0) REVERT: E 370 GLN cc_start: 0.8752 (mt0) cc_final: 0.8062 (tp40) REVERT: E 403 MET cc_start: 0.7757 (pmm) cc_final: 0.6868 (pmm) REVERT: E 431 GLU cc_start: 0.7376 (pt0) cc_final: 0.7139 (pt0) REVERT: E 462 LEU cc_start: 0.8968 (tt) cc_final: 0.8628 (mt) REVERT: E 464 MET cc_start: 0.8908 (tpp) cc_final: 0.8484 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0533 time to fit residues: 4.6962 Evaluate side-chains 45 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.156 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: 0.0056 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: 0.0092 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: 0.0170 chunk 41 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082935 restraints weight = 15064.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085015 restraints weight = 9305.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086502 restraints weight = 6314.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087619 restraints weight = 4622.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088361 restraints weight = 3561.262| |-----------------------------------------------------------------------------| r_work (final): 0.3416 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105432 restraints weight = 2792.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106323 restraints weight = 1458.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106590 restraints weight = 1109.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106594 restraints weight = 1007.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106594 restraints weight = 1005.082| |-----------------------------------------------------------------------------| r_work (final): 0.3842 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.079690 restraints weight = 2745.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080881 restraints weight = 1179.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081502 restraints weight = 612.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.081838 restraints weight = 359.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.082021 restraints weight = 239.879| |-----------------------------------------------------------------------------| r_work (final): 0.3323 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.090787 restraints weight = 5549.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.091381 restraints weight = 3052.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.091612 restraints weight = 2253.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.091612 restraints weight = 2048.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.091612 restraints weight = 2048.057| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4844 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= 0.132 Angle : 0.595 7.227 14758 Z= 0.330 Chirality : 0.037 0.123 1674 Planarity : 0.005 0.096 1450 Dihedral : 26.668 80.344 2342 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.27 (0.26), residues: 956 helix: -0.22 (0.23), residues: 514 sheet: -1.10 (0.61), residues: 70 loop : -1.56 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 477 TYR 0.021 0.001 TYR A 394 PHE 0.015 0.001 PHE A 317 TRP 0.007 0.001 TRP A 122 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00285 (10552) covalent geometry : angle 0.59517 (14758) hydrogen bonds : bond 0.09232 ( 521) hydrogen bonds : angle 4.83811 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.161 Fit side-chains REVERT: E 83 ASP cc_start: 0.7817 (m-30) cc_final: 0.7518 (m-30) REVERT: E 122 TRP cc_start: 0.8572 (p-90) cc_final: 0.7567 (p-90) REVERT: E 220 MET cc_start: 0.8288 (tpt) cc_final: 0.7194 (tpt) REVERT: E 250 MET cc_start: 0.8615 (ttm) cc_final: 0.7851 (ttm) REVERT: E 277 ILE cc_start: 0.9369 (mm) cc_final: 0.9136 (mm) REVERT: E 323 LEU cc_start: 0.6763 (pt) cc_final: 0.5274 (mt) REVERT: E 337 ASP cc_start: 0.7981 (p0) cc_final: 0.6415 (t0) REVERT: E 370 GLN cc_start: 0.8748 (mt0) cc_final: 0.8007 (tp40) REVERT: E 403 MET cc_start: 0.7740 (pmm) cc_final: 0.6833 (pmm) REVERT: E 462 LEU cc_start: 0.8918 (tt) cc_final: 0.8613 (mt) REVERT: E 464 MET cc_start: 0.8942 (tpp) cc_final: 0.8559 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0590 time to fit residues: 5.5973 Evaluate side-chains 45 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.120 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: 0.0030 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 : 0.003 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 : 0.004 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 : 0.005 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 : 0.007 ------------------------------------------------------------------------------- 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: 10.0000 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 0.1980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 13 optimal weight: 0.0170 chunk 97 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN E 413 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081715 restraints weight = 15368.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083760 restraints weight = 9446.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085247 restraints weight = 6411.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086357 restraints weight = 4684.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087082 restraints weight = 3605.701| |-----------------------------------------------------------------------------| r_work (final): 0.3388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.111840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.102935 restraints weight = 3186.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.104113 restraints weight = 1493.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104329 restraints weight = 1033.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104329 restraints weight = 950.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104329 restraints weight = 950.659| |-----------------------------------------------------------------------------| r_work (final): 0.3827 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.079801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077158 restraints weight = 2702.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078087 restraints weight = 695.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078585 restraints weight = 286.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078927 restraints weight = 157.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079079 restraints weight = 104.103| |-----------------------------------------------------------------------------| r_work (final): 0.3289 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092740 restraints weight = 6016.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093242 restraints weight = 2929.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093733 restraints weight = 2032.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093733 restraints weight = 1614.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093733 restraints weight = 1614.456| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10552 Z= 0.150 Angle : 0.605 7.346 14758 Z= 0.337 Chirality : 0.036 0.134 1674 Planarity : 0.004 0.055 1450 Dihedral : 26.614 81.356 2342 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.69 % Favored : 93.10 % 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: -1.39 (0.26), residues: 956 helix: -0.33 (0.23), residues: 514 sheet: -1.34 (0.60), residues: 70 loop : -1.55 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 437 TYR 0.012 0.001 TYR E 488 PHE 0.016 0.001 PHE E 317 TRP 0.065 0.004 TRP A 122 HIS 0.006 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00327 (10552) covalent geometry : angle 0.60483 (14758) hydrogen bonds : bond 0.09183 ( 521) hydrogen bonds : angle 4.92556 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1164.20 seconds wall clock time: 21 minutes 56.12 seconds (1316.12 seconds total)