Starting phenix.real_space_refine on Fri Feb 14 07:00:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqx_20455/02_2025/6pqx_20455.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqx_20455/02_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_20455/02_2025/6pqx_20455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqx_20455/02_2025/6pqx_20455.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqx_20455/02_2025/6pqx_20455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqx_20455/02_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-5592/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: 6.08, per 1000 atoms: 0.60 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: 2.80 Conformation dependent library (CDL) restraints added in 931.1 milliseconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 57.3% alpha, 13.8% beta 50 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 4.25 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: 4.41 Time building geometry restraints manager: 3.10 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: 0.05 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: 0.430 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.450 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- 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= 0.352 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 *********************** 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 : 0.013 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 : 0.010 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 : 0.384 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: 0.2100 time to fit residues: 24.6835 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 : 0.491 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: 0.0137 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 : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0274 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=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 = 0.111076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.109534 restraints weight = 3273.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110198 restraints weight = 1150.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.110467 restraints weight = 475.970| |-----------------------------------------------------------------------------| r_work (final): 0.3937 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078143 restraints weight = 15254.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080174 restraints weight = 9703.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081610 restraints weight = 6692.442| |-----------------------------------------------------------------------------| r_work (final): 0.3278 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071173 restraints weight = 2657.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072146 restraints weight = 918.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072751 restraints weight = 436.977| |-----------------------------------------------------------------------------| r_work (final): 0.3155 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085162 restraints weight = 6353.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085860 restraints weight = 2275.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086075 restraints weight = 1609.964| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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= 0.241 Angle : 0.715 8.738 14758 Z= 0.395 Chirality : 0.040 0.138 1674 Planarity : 0.005 0.048 1450 Dihedral : 27.619 85.380 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 A 41 HIS 0.006 0.001 HIS E 274 PHE 0.017 0.002 PHE E 344 TYR 0.008 0.002 TYR A 266 ARG 0.004 0.001 ARG E 443 *********************** 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 : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0126 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 78 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: E 119 ILE cc_start: 0.8940 (pt) cc_final: 0.8638 (mm) REVERT: E 250 MET cc_start: 0.8760 (ttm) cc_final: 0.7869 (ttm) REVERT: E 282 CYS cc_start: 0.8693 (p) cc_final: 0.8427 (p) REVERT: E 344 PHE cc_start: 0.8571 (t80) cc_final: 0.8211 (t80) REVERT: E 364 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7732 (mtp180) REVERT: E 370 GLN cc_start: 0.8745 (mt0) cc_final: 0.8371 (mt0) REVERT: E 403 MET cc_start: 0.8049 (pmm) cc_final: 0.7291 (pmm) REVERT: E 439 LYS cc_start: 0.8241 (tttt) cc_final: 0.8008 (tptt) REVERT: E 492 THR cc_start: 0.9058 (m) cc_final: 0.8793 (m) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2153 time to fit residues: 20.1583 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 : 0.447 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0143 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 : 0.019 ------------------------------------------------------------------------------- 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: 0.0970 chunk 68 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.8982 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.109966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.102118 restraints weight = 3177.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103231 restraints weight = 1564.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103822 restraints weight = 1121.535| |-----------------------------------------------------------------------------| r_work (final): 0.3809 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078139 restraints weight = 14984.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080198 restraints weight = 9248.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081603 restraints weight = 6255.883| |-----------------------------------------------------------------------------| r_work (final): 0.3291 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072756 restraints weight = 2825.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073922 restraints weight = 1229.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074536 restraints weight = 632.407| |-----------------------------------------------------------------------------| r_work (final): 0.3207 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084270 restraints weight = 5689.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084043 restraints weight = 3613.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084330 restraints weight = 2567.516| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10552 Z= 0.220 Angle : 0.669 7.422 14758 Z= 0.376 Chirality : 0.039 0.137 1674 Planarity : 0.005 0.057 1450 Dihedral : 27.414 82.207 2342 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.44 % Favored : 94.35 % 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: -1.60 (0.26), residues: 956 helix: -0.46 (0.22), residues: 508 sheet: -0.82 (0.64), residues: 62 loop : -1.84 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 41 HIS 0.006 0.002 HIS E 274 PHE 0.015 0.002 PHE A 317 TYR 0.007 0.001 TYR E 63 ARG 0.005 0.001 ARG A 485 *********************** 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 : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0123 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 70 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.454 Fit side-chains REVERT: E 250 MET cc_start: 0.8736 (ttm) cc_final: 0.8166 (ttm) REVERT: E 337 ASP cc_start: 0.7805 (p0) cc_final: 0.6560 (t0) REVERT: E 344 PHE cc_start: 0.8667 (t80) cc_final: 0.8394 (t80) REVERT: E 364 ARG cc_start: 0.8539 (mtp85) cc_final: 0.7711 (mtm-85) REVERT: E 370 GLN cc_start: 0.8560 (mt0) cc_final: 0.7986 (mm-40) REVERT: E 394 TYR cc_start: 0.7819 (t80) cc_final: 0.7521 (t80) REVERT: E 403 MET cc_start: 0.8027 (pmm) cc_final: 0.7223 (pmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1797 time to fit residues: 15.6207 Evaluate side-chains 47 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.468 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: 0.0143 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 : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0240 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 0.0980 chunk 59 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 179 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.110239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.103048 restraints weight = 3171.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.104308 restraints weight = 1524.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.104706 restraints weight = 1031.813| |-----------------------------------------------------------------------------| r_work (final): 0.3850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078723 restraints weight = 15047.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080810 restraints weight = 9182.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082299 restraints weight = 6203.521| |-----------------------------------------------------------------------------| r_work (final): 0.3295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074282 restraints weight = 2867.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.075479 restraints weight = 1210.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076052 restraints weight = 612.542| |-----------------------------------------------------------------------------| r_work (final): 0.3237 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087620 restraints weight = 6161.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088180 restraints weight = 2958.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088325 restraints weight = 2128.715| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10552 Z= 0.203 Angle : 0.646 7.381 14758 Z= 0.361 Chirality : 0.038 0.128 1674 Planarity : 0.004 0.043 1450 Dihedral : 27.397 89.470 2342 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.57 (0.26), residues: 956 helix: -0.34 (0.23), residues: 508 sheet: -1.00 (0.60), residues: 64 loop : -1.94 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 122 HIS 0.005 0.001 HIS E 274 PHE 0.031 0.002 PHE A 317 TYR 0.007 0.001 TYR A 63 ARG 0.003 0.001 ARG E 364 *********************** 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 : 0.010 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 : 0.012 Evaluate side-chains 68 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: E 250 MET cc_start: 0.8697 (ttm) cc_final: 0.8006 (ttm) REVERT: E 337 ASP cc_start: 0.7997 (p0) cc_final: 0.6457 (t0) REVERT: E 344 PHE cc_start: 0.8633 (t80) cc_final: 0.8323 (t80) REVERT: E 364 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7562 (mtm-85) REVERT: E 394 TYR cc_start: 0.7774 (t80) cc_final: 0.7485 (t80) REVERT: E 399 ASP cc_start: 0.8223 (p0) cc_final: 0.7699 (t0) REVERT: E 403 MET cc_start: 0.8023 (pmm) cc_final: 0.7286 (pmm) REVERT: E 492 THR cc_start: 0.8957 (m) cc_final: 0.8693 (m) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1547 time to fit residues: 13.3594 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 : 0.439 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0154 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 : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0260 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: 9.9990 chunk 58 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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** E 179 GLN E 413 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.109152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.101782 restraints weight = 3134.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102816 restraints weight = 1567.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103063 restraints weight = 1109.954| |-----------------------------------------------------------------------------| r_work (final): 0.3817 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078212 restraints weight = 14478.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080335 restraints weight = 8774.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081843 restraints weight = 5871.122| |-----------------------------------------------------------------------------| r_work (final): 0.3302 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074917 restraints weight = 2804.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075960 restraints weight = 1223.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076607 restraints weight = 637.975| |-----------------------------------------------------------------------------| r_work (final): 0.3258 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.092860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086076 restraints weight = 6024.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086672 restraints weight = 2660.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087095 restraints weight = 1862.442| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10552 Z= 0.213 Angle : 0.657 7.504 14758 Z= 0.365 Chirality : 0.038 0.141 1674 Planarity : 0.005 0.050 1450 Dihedral : 27.309 83.922 2342 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.32 % Favored : 92.47 % 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: -1.67 (0.25), residues: 956 helix: -0.45 (0.22), residues: 508 sheet: -1.02 (0.57), residues: 70 loop : -1.94 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 400 HIS 0.005 0.002 HIS E 216 PHE 0.028 0.002 PHE A 317 TYR 0.007 0.001 TYR A 63 ARG 0.005 0.001 ARG A 445 *********************** 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 : 0.010 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 : 0.009 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 : 0.457 Fit side-chains revert: symmetry clash REVERT: E 250 MET cc_start: 0.8657 (ttm) cc_final: 0.7964 (ttm) REVERT: E 337 ASP cc_start: 0.8115 (p0) cc_final: 0.6469 (t0) REVERT: E 344 PHE cc_start: 0.8664 (t80) cc_final: 0.8392 (t80) REVERT: E 403 MET cc_start: 0.7903 (pmm) cc_final: 0.7011 (pmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1638 time to fit residues: 14.3950 Evaluate side-chains 50 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.482 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: 0.0133 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 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: 0.0229 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 : 0.024 ------------------------------------------------------------------------------- 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: 7.9990 chunk 87 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 64 optimal weight: 0.0020 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.0050 chunk 75 optimal weight: 0.0770 overall best weight: 0.2560 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.112793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.105210 restraints weight = 3081.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.106311 restraints weight = 1568.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106598 restraints weight = 1114.558| |-----------------------------------------------------------------------------| r_work (final): 0.3879 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082705 restraints weight = 15092.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084957 restraints weight = 9390.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086514 restraints weight = 6386.620| |-----------------------------------------------------------------------------| r_work (final): 0.3368 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077148 restraints weight = 2685.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078229 restraints weight = 1159.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078825 restraints weight = 575.443| |-----------------------------------------------------------------------------| r_work (final): 0.3295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.098175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085601 restraints weight = 5824.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.086675 restraints weight = 2708.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.087198 restraints weight = 1783.251| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10552 Z= 0.174 Angle : 0.655 12.911 14758 Z= 0.355 Chirality : 0.038 0.147 1674 Planarity : 0.005 0.063 1450 Dihedral : 27.206 81.665 2342 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.65 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -1.49 (0.26), residues: 956 helix: -0.27 (0.23), residues: 508 sheet: -1.17 (0.56), residues: 70 loop : -1.87 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 122 HIS 0.005 0.001 HIS E 274 PHE 0.024 0.002 PHE A 317 TYR 0.017 0.001 TYR A 394 ARG 0.008 0.001 ARG E 437 *********************** 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 : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0117 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 80 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7743 (m-30) cc_final: 0.7465 (m-30) REVERT: E 122 TRP cc_start: 0.8884 (p-90) cc_final: 0.7706 (p-90) REVERT: E 250 MET cc_start: 0.8728 (ttm) cc_final: 0.7994 (ttm) REVERT: E 315 ASP cc_start: 0.8243 (m-30) cc_final: 0.7471 (p0) REVERT: E 318 LYS cc_start: 0.8694 (pttm) cc_final: 0.8256 (pmtt) REVERT: E 323 LEU cc_start: 0.6841 (pt) cc_final: 0.5370 (mt) REVERT: E 337 ASP cc_start: 0.8090 (p0) cc_final: 0.6518 (t0) REVERT: E 351 THR cc_start: 0.8448 (t) cc_final: 0.8097 (t) REVERT: E 364 ARG cc_start: 0.8387 (mtp85) cc_final: 0.7644 (mtm-85) REVERT: E 403 MET cc_start: 0.7946 (pmm) cc_final: 0.7005 (pmm) REVERT: E 462 LEU cc_start: 0.8964 (tt) cc_final: 0.8587 (mt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1640 time to fit residues: 16.4181 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 : 0.482 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: 0.0154 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 : 0.019 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 64 optimal weight: 0.0470 chunk 23 optimal weight: 7.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 274 HIS E 413 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.113129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105349 restraints weight = 3042.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.106249 restraints weight = 1667.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.107075 restraints weight = 1260.626| |-----------------------------------------------------------------------------| r_work (final): 0.3876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083220 restraints weight = 14934.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085440 restraints weight = 9018.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087051 restraints weight = 6038.859| |-----------------------------------------------------------------------------| r_work (final): 0.3386 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077339 restraints weight = 2800.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078183 restraints weight = 767.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078651 restraints weight = 333.972| |-----------------------------------------------------------------------------| r_work (final): 0.3326 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092257 restraints weight = 5620.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092755 restraints weight = 2490.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.092783 restraints weight = 1766.640| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10552 Z= 0.170 Angle : 0.619 7.430 14758 Z= 0.342 Chirality : 0.037 0.156 1674 Planarity : 0.004 0.041 1450 Dihedral : 26.982 82.699 2342 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.11 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.43 (0.25), residues: 956 helix: -0.27 (0.22), residues: 508 sheet: -1.09 (0.57), residues: 70 loop : -1.77 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 41 HIS 0.003 0.001 HIS A 483 PHE 0.020 0.001 PHE E 317 TYR 0.007 0.001 TYR E 62 ARG 0.004 0.000 ARG A 443 *********************** 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 : 0.011 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 : 0.010 Evaluate side-chains 80 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7783 (m-30) cc_final: 0.7501 (m-30) REVERT: E 122 TRP cc_start: 0.8390 (p-90) cc_final: 0.7677 (p-90) REVERT: E 220 MET cc_start: 0.8442 (tpt) cc_final: 0.7950 (tpt) REVERT: E 250 MET cc_start: 0.8779 (ttm) cc_final: 0.8038 (ttm) REVERT: E 337 ASP cc_start: 0.8128 (p0) cc_final: 0.6490 (t0) REVERT: E 364 ARG cc_start: 0.8435 (mtp85) cc_final: 0.7643 (mtm-85) REVERT: E 370 GLN cc_start: 0.8667 (mt0) cc_final: 0.7929 (tm-30) REVERT: E 403 MET cc_start: 0.7949 (pmm) cc_final: 0.7067 (pmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1811 time to fit residues: 17.7096 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 : 0.454 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: 0.0155 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 : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0258 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 0.0570 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.0270 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 68 optimal weight: 0.0870 chunk 56 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 100 optimal weight: 9.9990 overall best weight: 0.0732 ------------------------------------------------------------------------------- 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 ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3933 r_free = 0.3933 target = 0.115103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.106948 restraints weight = 3075.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.107762 restraints weight = 1635.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.108690 restraints weight = 1250.869| |-----------------------------------------------------------------------------| r_work (final): 0.3867 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084139 restraints weight = 14896.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086370 restraints weight = 9126.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088058 restraints weight = 6154.442| |-----------------------------------------------------------------------------| r_work (final): 0.3404 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079283 restraints weight = 2885.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080165 restraints weight = 822.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080672 restraints weight = 364.984| |-----------------------------------------------------------------------------| r_work (final): 0.3320 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088649 restraints weight = 5812.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.089645 restraints weight = 2581.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.090315 restraints weight = 1727.561| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10552 Z= 0.177 Angle : 0.622 7.198 14758 Z= 0.341 Chirality : 0.037 0.140 1674 Planarity : 0.004 0.035 1450 Dihedral : 26.782 79.124 2342 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.07 % Favored : 93.72 % 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: -1.38 (0.26), residues: 956 helix: -0.33 (0.22), residues: 508 sheet: -0.84 (0.58), residues: 70 loop : -1.64 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 41 HIS 0.003 0.001 HIS E 274 PHE 0.012 0.001 PHE E 180 TYR 0.016 0.001 TYR A 394 ARG 0.004 0.001 ARG E 437 *********************** 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 : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0151 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 81 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 122 TRP cc_start: 0.8522 (p-90) cc_final: 0.7588 (p-90) REVERT: E 220 MET cc_start: 0.8491 (tpt) cc_final: 0.7726 (tpt) REVERT: E 250 MET cc_start: 0.8602 (ttm) cc_final: 0.7758 (ttm) REVERT: E 277 ILE cc_start: 0.9328 (mm) cc_final: 0.9024 (mm) REVERT: E 337 ASP cc_start: 0.7926 (p0) cc_final: 0.6367 (t0) REVERT: E 364 ARG cc_start: 0.8334 (mtp85) cc_final: 0.7478 (mtm-85) REVERT: E 370 GLN cc_start: 0.8568 (mt0) cc_final: 0.7855 (tp40) REVERT: E 394 TYR cc_start: 0.7824 (t80) cc_final: 0.7539 (t80) REVERT: E 403 MET cc_start: 0.7742 (pmm) cc_final: 0.6635 (pmm) REVERT: E 426 ILE cc_start: 0.8592 (tt) cc_final: 0.8287 (tt) REVERT: E 448 HIS cc_start: 0.8056 (m90) cc_final: 0.7780 (m90) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1710 time to fit residues: 17.2707 Evaluate side-chains 54 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.454 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: 0.0151 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 : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0266 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 0.0370 chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.5862 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.112479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104093 restraints weight = 2803.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.105263 restraints weight = 1430.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.106015 restraints weight = 1027.945| |-----------------------------------------------------------------------------| r_work (final): 0.3833 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081414 restraints weight = 14459.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083529 restraints weight = 8818.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085074 restraints weight = 5921.374| |-----------------------------------------------------------------------------| r_work (final): 0.3368 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.080867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.078314 restraints weight = 2830.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079059 restraints weight = 776.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079550 restraints weight = 360.689| |-----------------------------------------------------------------------------| r_work (final): 0.3352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.098176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.085799 restraints weight = 5663.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086646 restraints weight = 2253.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087116 restraints weight = 1559.860| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4831 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= 0.207 Angle : 0.637 7.359 14758 Z= 0.353 Chirality : 0.037 0.150 1674 Planarity : 0.004 0.036 1450 Dihedral : 26.652 81.244 2342 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.04 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: -1.47 (0.26), residues: 956 helix: -0.35 (0.22), residues: 508 sheet: -1.39 (0.57), residues: 70 loop : -1.64 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP E 122 HIS 0.004 0.001 HIS E 413 PHE 0.017 0.001 PHE E 317 TYR 0.016 0.001 TYR A 394 ARG 0.004 0.001 ARG E 443 *********************** 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 : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0120 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 70 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7833 (m-30) cc_final: 0.7518 (m-30) REVERT: E 250 MET cc_start: 0.8611 (ttm) cc_final: 0.7808 (ttm) REVERT: E 277 ILE cc_start: 0.9319 (mm) cc_final: 0.9016 (mm) REVERT: E 337 ASP cc_start: 0.8270 (p0) cc_final: 0.6605 (t0) REVERT: E 364 ARG cc_start: 0.8407 (mtp85) cc_final: 0.7685 (mtp85) REVERT: E 403 MET cc_start: 0.7743 (pmm) cc_final: 0.6563 (pmm) REVERT: E 431 GLU cc_start: 0.7777 (pt0) cc_final: 0.7509 (pt0) REVERT: E 492 THR cc_start: 0.9211 (m) cc_final: 0.8794 (m) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1503 time to fit residues: 13.4949 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 : 0.452 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: 0.0142 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: 0.0238 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.0030 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 0.0170 chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 0.0770 chunk 25 optimal weight: 0.0980 chunk 80 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.111742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.109529 restraints weight = 3203.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.110441 restraints weight = 1465.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.111029 restraints weight = 722.028| |-----------------------------------------------------------------------------| r_work (final): 0.3982 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.095457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084519 restraints weight = 15082.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086693 restraints weight = 9458.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088268 restraints weight = 6440.978| |-----------------------------------------------------------------------------| r_work (final): 0.3422 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.084242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081107 restraints weight = 2647.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082344 restraints weight = 1189.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.083088 restraints weight = 654.269| |-----------------------------------------------------------------------------| r_work (final): 0.3388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091970 restraints weight = 5374.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.092440 restraints weight = 2920.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.092635 restraints weight = 2342.551| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10552 Z= 0.185 Angle : 0.644 7.239 14758 Z= 0.355 Chirality : 0.038 0.164 1674 Planarity : 0.005 0.082 1450 Dihedral : 26.561 79.318 2342 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.00 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: -1.70 (0.26), residues: 956 helix: -0.62 (0.22), residues: 512 sheet: -1.22 (0.57), residues: 70 loop : -1.69 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 122 HIS 0.001 0.000 HIS E 408 PHE 0.013 0.002 PHE A 292 TYR 0.020 0.001 TYR A 394 ARG 0.004 0.001 ARG A 477 ********************** 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: 0.0148 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 77 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: E 83 ASP cc_start: 0.7804 (m-30) cc_final: 0.7584 (m-30) REVERT: E 122 TRP cc_start: 0.8416 (p-90) cc_final: 0.7231 (p-90) REVERT: E 220 MET cc_start: 0.8335 (tpt) cc_final: 0.7707 (tpt) REVERT: E 250 MET cc_start: 0.8520 (ttm) cc_final: 0.7741 (ttm) REVERT: E 277 ILE cc_start: 0.9332 (mm) cc_final: 0.9023 (mm) REVERT: E 337 ASP cc_start: 0.8026 (p0) cc_final: 0.6397 (t0) REVERT: E 403 MET cc_start: 0.7818 (pmm) cc_final: 0.6848 (pmm) REVERT: E 426 ILE cc_start: 0.8654 (tt) cc_final: 0.8255 (tt) REVERT: E 431 GLU cc_start: 0.7538 (pt0) cc_final: 0.6915 (pt0) REVERT: E 448 HIS cc_start: 0.8022 (m90) cc_final: 0.7724 (m90) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1475 time to fit residues: 14.5878 Evaluate side-chains 47 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.448 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: 0.0139 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 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: 0.0238 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 98 optimal weight: 0.4980 chunk 68 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 97 optimal weight: 0.0870 chunk 39 optimal weight: 0.2980 overall best weight: 0.1890 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.115173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106632 restraints weight = 2929.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107455 restraints weight = 1560.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.107807 restraints weight = 1194.819| |-----------------------------------------------------------------------------| r_work (final): 0.3846 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086213 restraints weight = 15008.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088464 restraints weight = 9316.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090075 restraints weight = 6305.340| |-----------------------------------------------------------------------------| r_work (final): 0.3452 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081588 restraints weight = 2870.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.082671 restraints weight = 772.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.083122 restraints weight = 315.846| |-----------------------------------------------------------------------------| r_work (final): 0.3422 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.100783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093178 restraints weight = 5704.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.093748 restraints weight = 3303.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.094043 restraints weight = 2481.489| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10552 Z= 0.168 Angle : 0.632 7.480 14758 Z= 0.345 Chirality : 0.037 0.202 1674 Planarity : 0.005 0.077 1450 Dihedral : 26.437 81.105 2342 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.67 (0.26), residues: 956 helix: -0.64 (0.22), residues: 512 sheet: -1.03 (0.56), residues: 70 loop : -1.65 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 122 HIS 0.002 0.001 HIS A 285 PHE 0.013 0.001 PHE A 180 TYR 0.010 0.001 TYR A 266 ARG 0.004 0.001 ARG A 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.68 seconds wall clock time: 40 minutes 36.06 seconds (2436.06 seconds total)