Starting phenix.real_space_refine on Mon Jul 28 01:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqx_20455/07_2025/6pqx_20455.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqx_20455/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqx_20455/07_2025/6pqx_20455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqx_20455/07_2025/6pqx_20455.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqx_20455/07_2025/6pqx_20455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqx_20455/07_2025/6pqx_20455.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.53, per 1000 atoms: 0.65 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: 2.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 4.48 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: 4.20 Time building geometry restraints manager: 3.35 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'E' } 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 'B' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' } 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: 0.560 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.510 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- 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 : 15.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.003 TRP A 41 HIS 0.009 0.002 HIS A 216 PHE 0.028 0.002 PHE A 317 TYR 0.020 0.005 TYR A 59 ARG 0.042 0.007 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.16704 ( 521) hydrogen bonds : angle 7.21869 ( 1446) covalent geometry : bond 0.00605 (10552) covalent geometry : angle 0.98829 (14758) *********************** 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 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: 0.0146 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 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 : 0.415 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: 0.6846 (p) REVERT: A 169 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8104 (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: 0.6951 (tmm) REVERT: A 250 MET cc_start: 0.8661 (ttm) cc_final: 0.7668 (ttm) REVERT: A 344 PHE cc_start: 0.8858 (t80) cc_final: 0.8504 (t80) REVERT: A 364 ARG cc_start: 0.8467 (mtp85) cc_final: 0.7943 (mtp180) REVERT: A 403 MET cc_start: 0.7867 (pmm) cc_final: 0.6994 (pmm) REVERT: A 437 ARG cc_start: 0.8945 (tpp-160) cc_final: 0.8423 (tpp80) outliers start: 10 outliers final: 2 residues processed: 99 average time/residue: 0.1969 time to fit residues: 23.2272 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 : 0.486 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 : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0160 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 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 : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0273 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 : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.0370 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 overall best weight: 2.2462 ------------------------------------------------------------------------------- NQH flips ********* 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.111075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.109539 restraints weight = 3273.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.110145 restraints weight = 1115.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.110563 restraints weight = 538.672| |-----------------------------------------------------------------------------| r_work (final): 0.3938 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078142 restraints weight = 15255.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080180 restraints weight = 9703.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081599 restraints weight = 6688.096| |-----------------------------------------------------------------------------| r_work (final): 0.3277 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071175 restraints weight = 2657.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072140 restraints weight = 928.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072744 restraints weight = 439.899| |-----------------------------------------------------------------------------| r_work (final): 0.3155 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085144 restraints weight = 6353.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085843 restraints weight = 2313.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086044 restraints weight = 1648.070| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10552 Z= 0.180 Angle : 0.715 8.736 14758 Z= 0.395 Chirality : 0.040 0.138 1674 Planarity : 0.005 0.048 1450 Dihedral : 27.619 85.379 2342 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.35 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.25), residues: 956 helix: -0.62 (0.21), residues: 498 sheet: -1.26 (0.55), residues: 72 loop : -1.80 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 41 HIS 0.006 0.001 HIS E 274 PHE 0.017 0.002 PHE E 344 TYR 0.008 0.002 TYR E 266 ARG 0.004 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.09794 ( 521) hydrogen bonds : angle 5.60260 ( 1446) covalent geometry : bond 0.00398 (10552) covalent geometry : angle 0.71497 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0119 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 : 0.020 Evaluate side-chains 78 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: E 119 ILE cc_start: 0.8940 (pt) cc_final: 0.8640 (mm) REVERT: E 250 MET cc_start: 0.8762 (ttm) cc_final: 0.7869 (ttm) REVERT: E 282 CYS cc_start: 0.8694 (p) cc_final: 0.8428 (p) REVERT: E 344 PHE cc_start: 0.8572 (t80) cc_final: 0.8211 (t80) REVERT: E 364 ARG cc_start: 0.8412 (mtp85) cc_final: 0.7731 (mtp180) REVERT: E 370 GLN cc_start: 0.8745 (mt0) cc_final: 0.8372 (mt0) REVERT: E 403 MET cc_start: 0.8048 (pmm) cc_final: 0.7291 (pmm) REVERT: E 439 LYS cc_start: 0.8241 (tttt) cc_final: 0.8009 (tptt) REVERT: E 492 THR cc_start: 0.9058 (m) cc_final: 0.8792 (m) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2040 time to fit residues: 19.1507 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 : 0.525 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 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 : 0.011 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 : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0237 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 : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 0.0000 chunk 68 optimal weight: 0.0030 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4036 ------------------------------------------------------------------------------- NQH flips ********* 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... 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** 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.112216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.104193 restraints weight = 3096.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.105256 restraints weight = 1602.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.105528 restraints weight = 1131.575| |-----------------------------------------------------------------------------| r_work (final): 0.3820 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079266 restraints weight = 14209.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081415 restraints weight = 8669.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082870 restraints weight = 5802.232| |-----------------------------------------------------------------------------| r_work (final): 0.3323 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.071605 restraints weight = 2998.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.072598 restraints weight = 944.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073133 restraints weight = 414.889| |-----------------------------------------------------------------------------| r_work (final): 0.3226 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.094427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084790 restraints weight = 5512.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.085668 restraints weight = 2748.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.085289 restraints weight = 2034.055| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10552 Z= 0.155 Angle : 0.659 7.315 14758 Z= 0.368 Chirality : 0.038 0.143 1674 Planarity : 0.005 0.060 1450 Dihedral : 27.406 81.258 2342 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 956 helix: -0.37 (0.22), residues: 496 sheet: -0.82 (0.64), residues: 62 loop : -1.80 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 41 HIS 0.006 0.001 HIS E 274 PHE 0.014 0.002 PHE E 344 TYR 0.007 0.001 TYR A 63 ARG 0.004 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.09536 ( 521) hydrogen bonds : angle 5.23377 ( 1446) covalent geometry : bond 0.00336 (10552) covalent geometry : angle 0.65893 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0121 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 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 : 0.489 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.9237 (mt) cc_final: 0.8893 (mm) REVERT: E 83 ASP cc_start: 0.7720 (m-30) cc_final: 0.7396 (m-30) REVERT: E 119 ILE cc_start: 0.8905 (pt) cc_final: 0.8551 (mm) REVERT: E 250 MET cc_start: 0.8765 (ttm) cc_final: 0.8200 (ttm) REVERT: E 337 ASP cc_start: 0.7688 (p0) cc_final: 0.6460 (t0) REVERT: E 364 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7719 (mtp180) REVERT: E 370 GLN cc_start: 0.8575 (mt0) cc_final: 0.7960 (mm-40) REVERT: E 403 MET cc_start: 0.8094 (pmm) cc_final: 0.7282 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1801 time to fit residues: 16.7602 Evaluate side-chains 51 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.802 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 : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0175 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 : 0.015 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 : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0403 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 : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 29 optimal weight: 0.0270 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.111863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104092 restraints weight = 3140.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.105177 restraints weight = 1575.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105712 restraints weight = 1132.288| |-----------------------------------------------------------------------------| r_work (final): 0.3851 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079370 restraints weight = 15083.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081467 restraints weight = 9239.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082973 restraints weight = 6234.013| |-----------------------------------------------------------------------------| r_work (final): 0.3312 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074073 restraints weight = 2869.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075236 restraints weight = 1231.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075863 restraints weight = 639.212| |-----------------------------------------------------------------------------| r_work (final): 0.3233 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.095211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085314 restraints weight = 6190.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085801 restraints weight = 3014.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.085250 restraints weight = 2779.128| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10552 Z= 0.166 Angle : 0.663 7.398 14758 Z= 0.367 Chirality : 0.038 0.168 1674 Planarity : 0.004 0.045 1450 Dihedral : 27.361 88.471 2342 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.07 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.26), residues: 956 helix: -0.32 (0.23), residues: 510 sheet: -0.96 (0.60), residues: 64 loop : -1.95 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 400 HIS 0.005 0.001 HIS E 274 PHE 0.018 0.002 PHE A 317 TYR 0.015 0.001 TYR E 394 ARG 0.003 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.09599 ( 521) hydrogen bonds : angle 5.19113 ( 1446) covalent geometry : bond 0.00360 (10552) covalent geometry : angle 0.66277 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0263 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 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 : 0.513 Fit side-chains revert: symmetry clash REVERT: E 173 MET cc_start: 0.8682 (ttm) cc_final: 0.8479 (tpp) REVERT: E 250 MET cc_start: 0.8707 (ttm) cc_final: 0.7973 (ttm) REVERT: E 337 ASP cc_start: 0.7904 (p0) cc_final: 0.6466 (t0) REVERT: E 364 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7549 (mtm-85) REVERT: E 399 ASP cc_start: 0.8132 (p0) cc_final: 0.7484 (t0) REVERT: E 403 MET cc_start: 0.8045 (pmm) cc_final: 0.7147 (pmm) REVERT: E 492 THR cc_start: 0.8904 (m) cc_final: 0.8378 (m) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1595 time to fit residues: 15.2801 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 : 0.476 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: 0.0152 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 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 : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0262 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 : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.2408 ------------------------------------------------------------------------------- NQH flips ********* 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... 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** 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.112654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105297 restraints weight = 2972.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.106312 restraints weight = 1565.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.106604 restraints weight = 1119.813| |-----------------------------------------------------------------------------| r_work (final): 0.3878 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081414 restraints weight = 14465.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083589 restraints weight = 8980.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085105 restraints weight = 6085.652| |-----------------------------------------------------------------------------| r_work (final): 0.3357 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075874 restraints weight = 2757.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077097 restraints weight = 1198.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077763 restraints weight = 600.543| |-----------------------------------------------------------------------------| r_work (final): 0.3246 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.093838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089311 restraints weight = 6837.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089945 restraints weight = 2908.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090439 restraints weight = 1819.167| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3625 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= 0.142 Angle : 0.633 7.295 14758 Z= 0.350 Chirality : 0.037 0.128 1674 Planarity : 0.004 0.039 1450 Dihedral : 27.237 81.462 2342 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.26), residues: 956 helix: -0.23 (0.23), residues: 508 sheet: -0.56 (0.64), residues: 52 loop : -2.03 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 400 HIS 0.004 0.001 HIS E 274 PHE 0.018 0.002 PHE A 317 TYR 0.007 0.001 TYR A 398 ARG 0.009 0.001 ARG E 445 Details of bonding type rmsd hydrogen bonds : bond 0.09519 ( 521) hydrogen bonds : angle 5.04532 ( 1446) covalent geometry : bond 0.00303 (10552) covalent geometry : angle 0.63342 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0144 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 78 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.9187 (mt) cc_final: 0.8691 (mm) REVERT: E 83 ASP cc_start: 0.7883 (m-30) cc_final: 0.7486 (m-30) REVERT: E 122 TRP cc_start: 0.8729 (p-90) cc_final: 0.7049 (p-90) REVERT: E 220 MET cc_start: 0.8682 (mmm) cc_final: 0.8464 (mmm) REVERT: E 250 MET cc_start: 0.8781 (ttm) cc_final: 0.7979 (ttm) REVERT: E 315 ASP cc_start: 0.8425 (m-30) cc_final: 0.6781 (p0) REVERT: E 337 ASP cc_start: 0.7915 (p0) cc_final: 0.6555 (t0) REVERT: E 364 ARG cc_start: 0.8427 (mtp85) cc_final: 0.7479 (mtm-85) REVERT: E 370 GLN cc_start: 0.8578 (mt0) cc_final: 0.7963 (tp40) REVERT: E 403 MET cc_start: 0.8011 (pmm) cc_final: 0.7179 (pmm) REVERT: E 447 HIS cc_start: 0.7465 (m90) cc_final: 0.7136 (m90) REVERT: E 462 LEU cc_start: 0.8981 (tt) cc_final: 0.8663 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1798 time to fit residues: 17.1762 Evaluate side-chains 52 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.419 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0131 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0227 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 : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 0.0010 chunk 59 optimal weight: 7.9990 chunk 64 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 overall best weight: 0.2010 ------------------------------------------------------------------------------- NQH flips ********* 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.115346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.107736 restraints weight = 3003.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.108831 restraints weight = 1588.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.109082 restraints weight = 1164.944| |-----------------------------------------------------------------------------| r_work (final): 0.3894 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084177 restraints weight = 15127.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086510 restraints weight = 9223.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088104 restraints weight = 6193.614| |-----------------------------------------------------------------------------| r_work (final): 0.3404 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078714 restraints weight = 2694.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079919 restraints weight = 1233.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080522 restraints weight = 627.836| |-----------------------------------------------------------------------------| r_work (final): 0.3331 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088310 restraints weight = 5608.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.089028 restraints weight = 2708.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.089560 restraints weight = 2070.970| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10552 Z= 0.143 Angle : 0.646 7.570 14758 Z= 0.350 Chirality : 0.038 0.151 1674 Planarity : 0.005 0.076 1450 Dihedral : 27.056 82.551 2342 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.07 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 956 helix: -0.34 (0.22), residues: 514 sheet: -1.15 (0.63), residues: 64 loop : -1.86 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 122 HIS 0.007 0.001 HIS E 447 PHE 0.018 0.002 PHE E 317 TYR 0.017 0.001 TYR A 394 ARG 0.005 0.000 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.09441 ( 521) hydrogen bonds : angle 4.93348 ( 1446) covalent geometry : bond 0.00300 (10552) covalent geometry : angle 0.64578 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0144 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 84 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7797 (m-30) cc_final: 0.7542 (m-30) REVERT: E 250 MET cc_start: 0.8723 (ttm) cc_final: 0.7936 (ttm) REVERT: E 315 ASP cc_start: 0.8243 (m-30) cc_final: 0.7557 (p0) REVERT: E 318 LYS cc_start: 0.8686 (pttm) cc_final: 0.8245 (pttt) REVERT: E 337 ASP cc_start: 0.7819 (p0) cc_final: 0.6371 (t0) REVERT: E 370 GLN cc_start: 0.8524 (mt0) cc_final: 0.7821 (mm-40) REVERT: E 403 MET cc_start: 0.7794 (pmm) cc_final: 0.7107 (pmm) REVERT: E 462 LEU cc_start: 0.8892 (tt) cc_final: 0.8595 (mt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1421 time to fit residues: 15.2475 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.419 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0136 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0233 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 : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 0.0020 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 overall best weight: 4.2794 ------------------------------------------------------------------------------- NQH flips ********* 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.110788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.103137 restraints weight = 3092.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.104169 restraints weight = 1688.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.104859 restraints weight = 1234.564| |-----------------------------------------------------------------------------| r_work (final): 0.3841 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078863 restraints weight = 14462.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080882 restraints weight = 8897.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082318 restraints weight = 6030.266| |-----------------------------------------------------------------------------| r_work (final): 0.3307 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.074626 restraints weight = 2972.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075387 restraints weight = 864.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075889 restraints weight = 398.407| |-----------------------------------------------------------------------------| r_work (final): 0.3291 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085176 restraints weight = 5763.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.086150 restraints weight = 2630.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086646 restraints weight = 1787.264| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10552 Z= 0.199 Angle : 0.675 7.561 14758 Z= 0.369 Chirality : 0.039 0.205 1674 Planarity : 0.005 0.063 1450 Dihedral : 26.983 82.331 2342 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.49 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.26), residues: 956 helix: -0.53 (0.22), residues: 526 sheet: -1.30 (0.57), residues: 70 loop : -1.71 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 122 HIS 0.006 0.002 HIS E 274 PHE 0.022 0.002 PHE E 317 TYR 0.014 0.001 TYR E 73 ARG 0.007 0.001 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.09461 ( 521) hydrogen bonds : angle 5.12113 ( 1446) covalent geometry : bond 0.00423 (10552) covalent geometry : angle 0.67488 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0129 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 : 0.010 Evaluate side-chains 63 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7852 (m-30) cc_final: 0.7560 (m-30) REVERT: E 250 MET cc_start: 0.8721 (ttm) cc_final: 0.7923 (ttm) REVERT: E 315 ASP cc_start: 0.8443 (m-30) cc_final: 0.6834 (p0) REVERT: E 337 ASP cc_start: 0.8065 (p0) cc_final: 0.6365 (t0) REVERT: E 344 PHE cc_start: 0.8687 (t80) cc_final: 0.8455 (t80) REVERT: E 370 GLN cc_start: 0.8623 (mt0) cc_final: 0.8026 (tp40) REVERT: E 403 MET cc_start: 0.7814 (pmm) cc_final: 0.6861 (pmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1348 time to fit residues: 11.4497 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 : 0.495 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: 0.0150 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0230 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 : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.108920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101364 restraints weight = 3252.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102197 restraints weight = 1683.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.103051 restraints weight = 1197.244| |-----------------------------------------------------------------------------| r_work (final): 0.3824 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078168 restraints weight = 15241.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080236 restraints weight = 9520.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081681 restraints weight = 6530.022| |-----------------------------------------------------------------------------| r_work (final): 0.3278 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075374 restraints weight = 2663.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076296 restraints weight = 1053.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076872 restraints weight = 536.238| |-----------------------------------------------------------------------------| r_work (final): 0.3266 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.096250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086726 restraints weight = 5847.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086953 restraints weight = 2898.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.087177 restraints weight = 2583.725| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10552 Z= 0.205 Angle : 0.676 7.476 14758 Z= 0.373 Chirality : 0.039 0.189 1674 Planarity : 0.006 0.052 1450 Dihedral : 26.990 83.585 2342 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.11 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.25), residues: 956 helix: -0.86 (0.21), residues: 526 sheet: -1.69 (0.55), residues: 70 loop : -1.75 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 122 HIS 0.006 0.002 HIS A 274 PHE 0.023 0.002 PHE E 317 TYR 0.017 0.002 TYR A 394 ARG 0.008 0.001 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.09371 ( 521) hydrogen bonds : angle 5.20758 ( 1446) covalent geometry : bond 0.00437 (10552) covalent geometry : angle 0.67550 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0122 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 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: E 220 MET cc_start: 0.8744 (tpt) cc_final: 0.8420 (tpt) REVERT: E 250 MET cc_start: 0.8775 (ttm) cc_final: 0.8000 (ttm) REVERT: E 337 ASP cc_start: 0.8264 (p0) cc_final: 0.6459 (t0) REVERT: E 344 PHE cc_start: 0.8629 (t80) cc_final: 0.8423 (t80) REVERT: E 370 GLN cc_start: 0.8597 (mt0) cc_final: 0.8206 (tp40) REVERT: E 403 MET cc_start: 0.7839 (pmm) cc_final: 0.6801 (pmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1858 time to fit residues: 13.5954 Evaluate side-chains 42 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.439 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0135 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0271 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 : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* 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... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.113931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.105344 restraints weight = 2460.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.106417 restraints weight = 876.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.106968 restraints weight = 566.686| |-----------------------------------------------------------------------------| r_work (final): 0.3772 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080608 restraints weight = 14978.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082756 restraints weight = 9143.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084278 restraints weight = 6127.232| |-----------------------------------------------------------------------------| r_work (final): 0.3323 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075521 restraints weight = 2886.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.076317 restraints weight = 844.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076595 restraints weight = 371.262| |-----------------------------------------------------------------------------| r_work (final): 0.3301 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.085666 restraints weight = 5827.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086559 restraints weight = 2609.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.087020 restraints weight = 1741.743| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10552 Z= 0.153 Angle : 0.644 7.459 14758 Z= 0.352 Chirality : 0.038 0.165 1674 Planarity : 0.005 0.049 1450 Dihedral : 26.894 82.327 2342 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 956 helix: -0.55 (0.21), residues: 516 sheet: -1.48 (0.57), residues: 70 loop : -1.71 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.005 0.001 HIS A 274 PHE 0.018 0.001 PHE A 317 TYR 0.012 0.001 TYR A 73 ARG 0.005 0.001 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.09275 ( 521) hydrogen bonds : angle 5.00245 ( 1446) covalent geometry : bond 0.00332 (10552) covalent geometry : angle 0.64414 (14758) *********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0139 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 63 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 220 MET cc_start: 0.8733 (tpt) cc_final: 0.8404 (tpt) REVERT: E 250 MET cc_start: 0.8759 (ttm) cc_final: 0.8012 (ttm) REVERT: E 315 ASP cc_start: 0.8264 (m-30) cc_final: 0.6773 (p0) REVERT: E 337 ASP cc_start: 0.8296 (p0) cc_final: 0.6412 (t0) REVERT: E 370 GLN cc_start: 0.8571 (mt0) cc_final: 0.8084 (tp40) REVERT: E 403 MET cc_start: 0.7822 (pmm) cc_final: 0.6844 (pmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1663 time to fit residues: 13.2218 Evaluate side-chains 52 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.465 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0136 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0273 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 : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* 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... 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** 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.109786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.107733 restraints weight = 3211.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.108643 restraints weight = 1402.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.109126 restraints weight = 653.970| |-----------------------------------------------------------------------------| r_work (final): 0.3966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083974 restraints weight = 14452.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086237 restraints weight = 8731.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088005 restraints weight = 6187.240| |-----------------------------------------------------------------------------| r_work (final): 0.3411 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.083696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080463 restraints weight = 2606.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081776 restraints weight = 1204.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082551 restraints weight = 672.982| |-----------------------------------------------------------------------------| r_work (final): 0.3376 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087307 restraints weight = 5714.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088093 restraints weight = 2526.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088675 restraints weight = 1788.335| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10552 Z= 0.139 Angle : 0.647 7.460 14758 Z= 0.350 Chirality : 0.038 0.154 1674 Planarity : 0.004 0.045 1450 Dihedral : 26.797 80.593 2342 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.26), residues: 956 helix: -0.41 (0.22), residues: 514 sheet: -1.63 (0.57), residues: 66 loop : -1.75 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 122 HIS 0.004 0.001 HIS E 274 PHE 0.014 0.002 PHE E 317 TYR 0.020 0.002 TYR A 394 ARG 0.013 0.001 ARG E 342 Details of bonding type rmsd hydrogen bonds : bond 0.09262 ( 521) hydrogen bonds : angle 4.96995 ( 1446) covalent geometry : bond 0.00303 (10552) covalent geometry : angle 0.64744 (14758) ********************** 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0153 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 : 0.010 Evaluate side-chains 75 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7868 (m-30) cc_final: 0.7620 (m-30) REVERT: E 220 MET cc_start: 0.8555 (tpt) cc_final: 0.8064 (tpt) REVERT: E 250 MET cc_start: 0.8656 (ttm) cc_final: 0.7915 (ttm) REVERT: E 315 ASP cc_start: 0.8237 (m-30) cc_final: 0.6755 (p0) REVERT: E 323 LEU cc_start: 0.6992 (pt) cc_final: 0.6552 (tt) REVERT: E 337 ASP cc_start: 0.7992 (p0) cc_final: 0.6370 (t0) REVERT: E 370 GLN cc_start: 0.8542 (mt0) cc_final: 0.8104 (tp40) REVERT: E 403 MET cc_start: 0.7738 (pmm) cc_final: 0.6809 (pmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1538 time to fit residues: 14.6189 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.473 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: 0.0152 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 : 0.013 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 : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0267 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 : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 6.9990 chunk 68 optimal weight: 0.0070 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.109698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.103191 restraints weight = 2923.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103931 restraints weight = 1612.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.104069 restraints weight = 1269.356| |-----------------------------------------------------------------------------| r_work (final): 0.3788 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081255 restraints weight = 14738.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083342 restraints weight = 8854.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085278 restraints weight = 6336.049| |-----------------------------------------------------------------------------| r_work (final): 0.3359 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.079483 restraints weight = 2804.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080903 restraints weight = 1191.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.081668 restraints weight = 645.946| |-----------------------------------------------------------------------------| r_work (final): 0.3365 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.099152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090571 restraints weight = 5919.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091693 restraints weight = 3319.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.091224 restraints weight = 2371.708| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4814 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= 0.154 Angle : 0.639 7.365 14758 Z= 0.351 Chirality : 0.038 0.162 1674 Planarity : 0.004 0.042 1450 Dihedral : 26.763 80.390 2342 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.86 % Favored : 93.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 956 helix: -0.42 (0.22), residues: 514 sheet: -1.45 (0.61), residues: 70 loop : -1.66 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 122 HIS 0.005 0.001 HIS E 274 PHE 0.018 0.002 PHE A 317 TYR 0.010 0.001 TYR E 73 ARG 0.007 0.001 ARG E 342 Details of bonding type rmsd hydrogen bonds : bond 0.09204 ( 521) hydrogen bonds : angle 4.97772 ( 1446) covalent geometry : bond 0.00335 (10552) covalent geometry : angle 0.63946 (14758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.79 seconds wall clock time: 55 minutes 13.85 seconds (3313.85 seconds total)