Starting phenix.real_space_refine on Fri Jul 3 19:24:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx6_44995/07_2026/9bx6_44995_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx6_44995/07_2026/9bx6_44995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bx6_44995/07_2026/9bx6_44995_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx6_44995/07_2026/9bx6_44995_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bx6_44995/07_2026/9bx6_44995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx6_44995/07_2026/9bx6_44995.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.72, per 1000 atoms: 0.23 Number of scatterers: 15954 At special positions: 0 Unit cell: (94.024, 136.948, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 719.8 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.058A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.274A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.547A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.737A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.889A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.457A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4936 1.34 - 1.46: 2932 1.46 - 1.58: 8255 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.38e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 21464 2.11 - 4.22: 467 4.22 - 6.33: 58 6.33 - 8.44: 8 8.44 - 10.55: 7 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.68 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.51 3.68 1.06e+00 8.90e-01 1.21e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8642 17.66 - 35.31: 855 35.31 - 52.97: 255 52.97 - 70.63: 64 70.63 - 88.28: 40 Dihedral angle restraints: 9856 sinusoidal: 4110 harmonic: 5746 Sorted by residual: dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.30 12.30 0 2.50e+00 1.60e-01 2.42e+01 dihedral pdb=" N VAL C 125 " pdb=" C VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual 123.40 135.54 -12.14 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" C ASN C 98 " pdb=" N ASN C 98 " pdb=" CA ASN C 98 " pdb=" CB ASN C 98 " ideal model delta harmonic sigma weight residual -122.60 -134.24 11.64 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2123 0.093 - 0.185: 185 0.185 - 0.278: 32 0.278 - 0.371: 6 0.371 - 0.464: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 7 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11864 3.11 - 3.70: 26421 3.70 - 4.30: 41219 4.30 - 4.90: 64952 Nonbonded interactions: 144588 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 3.060 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 ... (remaining 144583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.150 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.009 0.833 16299 Z= 0.732 Angle : 0.756 10.552 22004 Z= 0.461 Chirality : 0.059 0.464 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.909 88.283 6168 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE D 92 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.33 (16298) covalent geometry : angle 0.75623 / 0.46 (22004) hydrogen bonds : bond 0.16166 / 10.52 ( 896) hydrogen bonds : angle 6.35133 / 4.47 ( 2616) Misc. bond : bond 0.83331 / 43.86 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 765 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.6946 (m90) cc_final: 0.6572 (m90) REVERT: A 172 LEU cc_start: 0.9000 (mp) cc_final: 0.8766 (mp) REVERT: A 231 ASP cc_start: 0.8049 (t70) cc_final: 0.7848 (t0) REVERT: A 584 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8404 (tp) REVERT: B 40 TYR cc_start: 0.8191 (t80) cc_final: 0.7943 (t80) REVERT: B 172 LEU cc_start: 0.9229 (mp) cc_final: 0.9014 (mp) REVERT: B 309 GLU cc_start: 0.7790 (tp30) cc_final: 0.7493 (tp30) REVERT: B 362 ASP cc_start: 0.7788 (m-30) cc_final: 0.7540 (m-30) REVERT: B 375 LYS cc_start: 0.8497 (mptp) cc_final: 0.8283 (mmtt) REVERT: C 47 LEU cc_start: 0.1019 (mt) cc_final: 0.0744 (mt) REVERT: C 273 PHE cc_start: 0.1305 (m-80) cc_final: 0.0989 (t80) REVERT: C 286 VAL cc_start: 0.4277 (t) cc_final: 0.3500 (p) outliers start: 24 outliers final: 6 residues processed: 771 average time/residue: 0.1431 time to fit residues: 160.1214 Evaluate side-chains 486 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 479 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 14 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 668 ASN B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 234 GLN C 249 GLN D 24 GLN D 28 GLN D 186 GLN D 238 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.092368 restraints weight = 25908.261| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.90 r_work: 0.2717 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16299 Z= 0.310 Angle : 0.703 12.958 22004 Z= 0.373 Chirality : 0.047 0.343 2348 Planarity : 0.004 0.053 2812 Dihedral : 7.389 70.307 2276 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.85 % Allowed : 17.21 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 1928 helix: 1.47 (0.15), residues: 1121 sheet: 0.14 (0.39), residues: 148 loop : 0.75 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 331 TYR 0.024 0.002 TYR C 173 PHE 0.034 0.002 PHE A 100 TRP 0.024 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.31 (16298) covalent geometry : angle 0.70313 / 0.37 (22004) hydrogen bonds : bond 0.04891 / 3.14 ( 896) hydrogen bonds : angle 5.26247 / 3.69 ( 2616) Misc. bond : bond 0.00306 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 528 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8739 (m90) cc_final: 0.8185 (m90) REVERT: A 67 GLU cc_start: 0.8812 (mp0) cc_final: 0.8379 (mp0) REVERT: A 274 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8194 (ttm-80) REVERT: A 336 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9278 (mtpp) REVERT: A 383 SER cc_start: 0.9460 (m) cc_final: 0.9227 (t) REVERT: A 394 TYR cc_start: 0.9399 (m-80) cc_final: 0.9059 (m-80) REVERT: A 444 ASP cc_start: 0.8124 (t70) cc_final: 0.7872 (t70) REVERT: A 548 GLU cc_start: 0.8779 (tp30) cc_final: 0.8459 (tp30) REVERT: A 598 MET cc_start: 0.9080 (ttm) cc_final: 0.8749 (mtt) REVERT: A 628 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8672 (mt-10) REVERT: A 659 LYS cc_start: 0.8857 (pttp) cc_final: 0.8647 (pttp) REVERT: B 31 GLU cc_start: 0.8858 (mp0) cc_final: 0.8329 (pm20) REVERT: B 56 ASP cc_start: 0.9012 (m-30) cc_final: 0.8636 (m-30) REVERT: B 64 TYR cc_start: 0.9249 (m-10) cc_final: 0.8754 (m-10) REVERT: B 109 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8475 (m110) REVERT: B 116 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 148 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 276 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8958 (mtpp) REVERT: B 474 GLN cc_start: 0.9278 (mt0) cc_final: 0.9075 (mt0) REVERT: B 493 MET cc_start: 0.9574 (tmm) cc_final: 0.9309 (tmm) REVERT: B 586 TYR cc_start: 0.9385 (m-80) cc_final: 0.9066 (m-80) REVERT: B 628 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 681 THR cc_start: 0.9411 (p) cc_final: 0.9119 (p) REVERT: B 686 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8160 (ttm-80) REVERT: C 28 GLN cc_start: 0.8704 (mm110) cc_final: 0.8500 (mm110) REVERT: C 47 LEU cc_start: 0.5317 (mt) cc_final: 0.4697 (tp) REVERT: C 157 MET cc_start: 0.9205 (mtm) cc_final: 0.8644 (ptt) REVERT: C 178 PHE cc_start: 0.7952 (m-80) cc_final: 0.7455 (m-80) REVERT: C 184 LEU cc_start: 0.4953 (mt) cc_final: 0.4080 (pp) REVERT: C 193 LEU cc_start: 0.7979 (mt) cc_final: 0.7574 (tp) REVERT: C 203 VAL cc_start: 0.7628 (t) cc_final: 0.7147 (t) REVERT: C 224 LEU cc_start: 0.9093 (mt) cc_final: 0.8888 (mt) REVERT: C 236 TYR cc_start: 0.8441 (t80) cc_final: 0.8221 (t80) REVERT: C 270 ASN cc_start: 0.7738 (m-40) cc_final: 0.7410 (t0) REVERT: C 273 PHE cc_start: 0.6395 (m-80) cc_final: 0.5809 (m-10) REVERT: C 282 ILE cc_start: 0.4011 (tt) cc_final: 0.3721 (tp) REVERT: C 315 LEU cc_start: 0.9334 (mt) cc_final: 0.9123 (mt) REVERT: D 31 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7000 (pp) REVERT: D 51 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6288 (mm-30) REVERT: D 183 LYS cc_start: 0.8463 (mttt) cc_final: 0.8183 (tptt) REVERT: D 242 TYR cc_start: 0.7794 (t80) cc_final: 0.7360 (t80) outliers start: 66 outliers final: 30 residues processed: 561 average time/residue: 0.1165 time to fit residues: 97.1195 Evaluate side-chains 459 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 425 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 232 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 24 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.095690 restraints weight = 26101.294| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.92 r_work: 0.2765 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16299 Z= 0.150 Angle : 0.601 13.126 22004 Z= 0.322 Chirality : 0.043 0.256 2348 Planarity : 0.004 0.059 2812 Dihedral : 6.933 63.357 2266 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.98 % Allowed : 19.43 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1928 helix: 1.34 (0.15), residues: 1134 sheet: 0.14 (0.40), residues: 140 loop : 0.69 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 196 TYR 0.027 0.001 TYR C 173 PHE 0.027 0.002 PHE C 172 TRP 0.009 0.001 TRP A 9 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16298) covalent geometry : angle 0.60072 / 0.32 (22004) hydrogen bonds : bond 0.04237 / 2.72 ( 896) hydrogen bonds : angle 5.05940 / 3.56 ( 2616) Misc. bond : bond 0.00361 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 493 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8666 (m90) cc_final: 0.8324 (m-70) REVERT: A 64 TYR cc_start: 0.9252 (m-10) cc_final: 0.8841 (m-10) REVERT: A 104 TYR cc_start: 0.9395 (m-80) cc_final: 0.8937 (m-80) REVERT: A 172 LEU cc_start: 0.9516 (mp) cc_final: 0.8933 (mp) REVERT: A 178 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.8831 (p) REVERT: A 228 LYS cc_start: 0.9325 (mtpp) cc_final: 0.8952 (mtpp) REVERT: A 232 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.9042 (m110) REVERT: A 266 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8773 (mtmm) REVERT: A 274 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.7598 (tpp80) REVERT: A 334 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8584 (ptpt) REVERT: A 336 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9229 (mmtt) REVERT: A 350 ARG cc_start: 0.9417 (mtp85) cc_final: 0.8614 (mtp85) REVERT: A 394 TYR cc_start: 0.9430 (m-80) cc_final: 0.9165 (m-80) REVERT: A 406 ASP cc_start: 0.8379 (m-30) cc_final: 0.7964 (t0) REVERT: B 31 GLU cc_start: 0.8873 (mp0) cc_final: 0.8342 (pm20) REVERT: B 52 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8739 (tptm) REVERT: B 56 ASP cc_start: 0.9027 (m-30) cc_final: 0.8520 (m-30) REVERT: B 64 TYR cc_start: 0.9199 (m-10) cc_final: 0.8702 (m-10) REVERT: B 75 GLU cc_start: 0.8452 (mp0) cc_final: 0.8111 (mp0) REVERT: B 79 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8263 (mm-30) REVERT: B 232 ASN cc_start: 0.9171 (m-40) cc_final: 0.8854 (m110) REVERT: B 274 ARG cc_start: 0.8088 (ptp90) cc_final: 0.6866 (ptp-170) REVERT: B 276 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8780 (mmtt) REVERT: B 320 ASN cc_start: 0.8687 (m-40) cc_final: 0.8364 (m-40) REVERT: B 493 MET cc_start: 0.9560 (tmm) cc_final: 0.9346 (tmm) REVERT: B 586 TYR cc_start: 0.9324 (m-80) cc_final: 0.9114 (m-80) REVERT: B 628 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 681 THR cc_start: 0.9255 (p) cc_final: 0.9022 (p) REVERT: B 686 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8145 (ttm-80) REVERT: C 93 MET cc_start: 0.8024 (mtt) cc_final: 0.7707 (mtt) REVERT: C 157 MET cc_start: 0.9330 (mtm) cc_final: 0.8965 (ptt) REVERT: C 169 TYR cc_start: 0.8643 (m-80) cc_final: 0.8382 (m-80) REVERT: C 181 GLN cc_start: 0.7741 (mp10) cc_final: 0.7447 (mp10) REVERT: C 193 LEU cc_start: 0.7891 (mt) cc_final: 0.7548 (tp) REVERT: C 203 VAL cc_start: 0.7557 (t) cc_final: 0.7171 (t) REVERT: C 212 ILE cc_start: 0.7433 (mm) cc_final: 0.7158 (mm) REVERT: C 259 PHE cc_start: 0.7376 (t80) cc_final: 0.7171 (t80) REVERT: C 270 ASN cc_start: 0.7734 (m-40) cc_final: 0.7499 (t0) REVERT: D 44 TRP cc_start: 0.7469 (t-100) cc_final: 0.7254 (t-100) REVERT: D 47 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7332 (mm) REVERT: D 178 PHE cc_start: 0.7501 (m-80) cc_final: 0.7241 (m-80) REVERT: D 183 LYS cc_start: 0.8493 (mttt) cc_final: 0.8145 (tptt) REVERT: D 242 TYR cc_start: 0.7730 (t80) cc_final: 0.7333 (t80) REVERT: D 282 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7402 (mm) outliers start: 51 outliers final: 25 residues processed: 525 average time/residue: 0.1252 time to fit residues: 98.3142 Evaluate side-chains 469 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 436 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 147 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 645 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.090350 restraints weight = 26160.272| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.89 r_work: 0.2683 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 16299 Z= 0.345 Angle : 0.682 12.887 22004 Z= 0.361 Chirality : 0.046 0.263 2348 Planarity : 0.004 0.058 2812 Dihedral : 7.266 64.742 2266 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.03 % Allowed : 19.31 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1928 helix: 1.23 (0.15), residues: 1144 sheet: -0.38 (0.40), residues: 140 loop : 0.59 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 261 TYR 0.017 0.002 TYR C 173 PHE 0.024 0.002 PHE C 172 TRP 0.014 0.002 TRP B 9 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00775 / 0.34 (16298) covalent geometry : angle 0.68229 / 0.36 (22004) hydrogen bonds : bond 0.04399 / 2.82 ( 896) hydrogen bonds : angle 5.27282 / 3.71 ( 2616) Misc. bond : bond 0.00428 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 442 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8790 (m90) cc_final: 0.8562 (m-70) REVERT: A 144 MET cc_start: 0.9274 (mtm) cc_final: 0.9033 (mtp) REVERT: A 178 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 266 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8830 (mtmm) REVERT: A 274 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8346 (ttm-80) REVERT: A 334 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8775 (ptpt) REVERT: A 384 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: A 659 LYS cc_start: 0.9034 (pttp) cc_final: 0.8803 (pttp) REVERT: A 684 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7653 (t80) REVERT: B 31 GLU cc_start: 0.8924 (mp0) cc_final: 0.8420 (mp0) REVERT: B 52 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8767 (tptm) REVERT: B 56 ASP cc_start: 0.9065 (m-30) cc_final: 0.8603 (m-30) REVERT: B 79 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 148 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8477 (mt-10) REVERT: B 150 GLN cc_start: 0.9287 (tp-100) cc_final: 0.8987 (tp-100) REVERT: B 232 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.9029 (m-40) REVERT: B 274 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7003 (ptp-170) REVERT: B 276 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8915 (mmtt) REVERT: B 586 TYR cc_start: 0.9389 (m-80) cc_final: 0.9100 (m-80) REVERT: B 588 GLN cc_start: 0.9324 (mm-40) cc_final: 0.9088 (mm-40) REVERT: B 589 SER cc_start: 0.9677 (OUTLIER) cc_final: 0.9344 (p) REVERT: B 686 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8248 (ttm-80) REVERT: C 134 LYS cc_start: 0.7481 (ptpp) cc_final: 0.7102 (ptpp) REVERT: C 137 MET cc_start: 0.6729 (mmt) cc_final: 0.6378 (mpp) REVERT: C 157 MET cc_start: 0.9311 (mtm) cc_final: 0.9011 (ptm) REVERT: C 174 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7283 (t80) REVERT: C 181 GLN cc_start: 0.7626 (mp-120) cc_final: 0.7283 (mp10) REVERT: C 193 LEU cc_start: 0.7827 (mt) cc_final: 0.7550 (tp) REVERT: C 203 VAL cc_start: 0.8026 (t) cc_final: 0.7726 (t) REVERT: C 236 TYR cc_start: 0.7348 (t80) cc_final: 0.6873 (t80) REVERT: C 270 ASN cc_start: 0.8142 (m-40) cc_final: 0.7919 (t0) REVERT: D 196 ARG cc_start: 0.6160 (tmm-80) cc_final: 0.5945 (ptm-80) REVERT: D 242 TYR cc_start: 0.7981 (t80) cc_final: 0.7526 (t80) REVERT: D 282 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7477 (mm) outliers start: 69 outliers final: 37 residues processed: 479 average time/residue: 0.1295 time to fit residues: 92.5886 Evaluate side-chains 451 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 403 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 164 optimal weight: 0.0770 chunk 189 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 361 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 91 ASN D 101 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.096842 restraints weight = 25663.957| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.95 r_work: 0.2789 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16299 Z= 0.136 Angle : 0.581 12.642 22004 Z= 0.305 Chirality : 0.042 0.233 2348 Planarity : 0.004 0.054 2812 Dihedral : 6.782 60.175 2266 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.57 % Allowed : 21.30 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1928 helix: 1.32 (0.15), residues: 1138 sheet: -0.45 (0.40), residues: 152 loop : 0.43 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.024 0.001 TYR D 174 PHE 0.039 0.002 PHE C 259 TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16298) covalent geometry : angle 0.58088 / 0.30 (22004) hydrogen bonds : bond 0.03830 / 2.45 ( 896) hydrogen bonds : angle 5.00559 / 3.51 ( 2616) Misc. bond : bond 0.00595 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 474 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.9357 (m-80) cc_final: 0.8924 (m-80) REVERT: A 178 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 228 LYS cc_start: 0.9350 (mtpp) cc_final: 0.9121 (mtpt) REVERT: A 232 ASN cc_start: 0.9201 (m110) cc_final: 0.8966 (m110) REVERT: A 266 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8751 (mtmm) REVERT: A 274 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8247 (ttm-80) REVERT: A 286 ASP cc_start: 0.8793 (m-30) cc_final: 0.8449 (m-30) REVERT: A 334 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8725 (ptpt) REVERT: A 362 ASP cc_start: 0.8621 (m-30) cc_final: 0.8233 (m-30) REVERT: A 406 ASP cc_start: 0.8482 (m-30) cc_final: 0.8258 (m-30) REVERT: A 444 ASP cc_start: 0.8390 (t70) cc_final: 0.8098 (t70) REVERT: A 595 MET cc_start: 0.8935 (mmm) cc_final: 0.8661 (mmt) REVERT: A 659 LYS cc_start: 0.8973 (pttp) cc_final: 0.8733 (pttp) REVERT: A 684 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 31 GLU cc_start: 0.8919 (mp0) cc_final: 0.8424 (mp0) REVERT: B 52 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.8830 (tptt) REVERT: B 56 ASP cc_start: 0.9016 (m-30) cc_final: 0.8569 (m-30) REVERT: B 75 GLU cc_start: 0.8508 (mp0) cc_final: 0.8227 (mp0) REVERT: B 79 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 184 ARG cc_start: 0.9226 (tpp-160) cc_final: 0.8945 (tpp80) REVERT: B 232 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.8943 (m-40) REVERT: B 274 ARG cc_start: 0.8185 (ptp90) cc_final: 0.7132 (ptp-170) REVERT: B 276 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8828 (mmtt) REVERT: B 320 ASN cc_start: 0.8531 (m-40) cc_final: 0.8192 (m-40) REVERT: B 361 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: B 474 GLN cc_start: 0.9017 (mt0) cc_final: 0.8791 (mt0) REVERT: B 586 TYR cc_start: 0.9279 (m-80) cc_final: 0.9005 (m-80) REVERT: B 628 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8347 (mt-10) REVERT: B 686 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8227 (ttm-80) REVERT: C 109 PHE cc_start: 0.8235 (m-10) cc_final: 0.7834 (m-10) REVERT: C 134 LYS cc_start: 0.7434 (ptpp) cc_final: 0.7211 (ptpp) REVERT: C 137 MET cc_start: 0.7127 (mmt) cc_final: 0.6765 (mpp) REVERT: C 157 MET cc_start: 0.9320 (mtm) cc_final: 0.8919 (ptt) REVERT: C 174 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7189 (t80) REVERT: C 181 GLN cc_start: 0.7703 (mp-120) cc_final: 0.7342 (mp10) REVERT: C 193 LEU cc_start: 0.7720 (mt) cc_final: 0.7484 (tt) REVERT: C 203 VAL cc_start: 0.8053 (t) cc_final: 0.7751 (t) REVERT: C 236 TYR cc_start: 0.7913 (t80) cc_final: 0.7271 (t80) REVERT: C 269 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8501 (ptt) REVERT: C 270 ASN cc_start: 0.8188 (m-40) cc_final: 0.7959 (t0) REVERT: D 150 GLU cc_start: 0.5448 (tp30) cc_final: 0.4978 (mm-30) REVERT: D 242 TYR cc_start: 0.7855 (t80) cc_final: 0.7442 (t80) outliers start: 44 outliers final: 17 residues processed: 495 average time/residue: 0.1215 time to fit residues: 91.0207 Evaluate side-chains 455 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 429 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 0.0370 chunk 84 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN C 132 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096304 restraints weight = 25597.127| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.92 r_work: 0.2777 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16299 Z= 0.159 Angle : 0.590 12.422 22004 Z= 0.308 Chirality : 0.042 0.158 2348 Planarity : 0.004 0.057 2812 Dihedral : 6.648 61.592 2264 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.74 % Allowed : 20.89 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 1928 helix: 1.37 (0.15), residues: 1135 sheet: -0.48 (0.40), residues: 156 loop : 0.41 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 196 TYR 0.030 0.001 TYR D 174 PHE 0.034 0.002 PHE C 259 TRP 0.010 0.001 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16298) covalent geometry : angle 0.58976 / 0.31 (22004) hydrogen bonds : bond 0.03800 / 2.43 ( 896) hydrogen bonds : angle 5.00811 / 3.52 ( 2616) Misc. bond : bond 0.00550 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 451 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8636 (m-70) cc_final: 0.8390 (m90) REVERT: A 104 TYR cc_start: 0.9369 (m-80) cc_final: 0.8914 (m-80) REVERT: A 178 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8846 (p) REVERT: A 228 LYS cc_start: 0.9345 (mtpp) cc_final: 0.9109 (mtpt) REVERT: A 266 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8776 (mtmm) REVERT: A 274 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8408 (ttm-80) REVERT: A 286 ASP cc_start: 0.8811 (m-30) cc_final: 0.8424 (m-30) REVERT: A 334 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8744 (ptpt) REVERT: A 406 ASP cc_start: 0.8480 (m-30) cc_final: 0.8235 (m-30) REVERT: A 446 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8135 (mmm160) REVERT: A 595 MET cc_start: 0.9022 (mmm) cc_final: 0.8780 (mmt) REVERT: A 684 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 31 GLU cc_start: 0.8926 (mp0) cc_final: 0.8418 (mp0) REVERT: B 52 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.8839 (tptt) REVERT: B 56 ASP cc_start: 0.9011 (m-30) cc_final: 0.8552 (m-30) REVERT: B 75 GLU cc_start: 0.8486 (mp0) cc_final: 0.8214 (mp0) REVERT: B 79 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 211 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8120 (mm-30) REVERT: B 274 ARG cc_start: 0.8144 (ptp90) cc_final: 0.7088 (ptp-170) REVERT: B 276 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8831 (mmtt) REVERT: B 320 ASN cc_start: 0.8511 (m-40) cc_final: 0.8215 (m-40) REVERT: B 359 MET cc_start: 0.9413 (ttp) cc_final: 0.9133 (tmm) REVERT: B 474 GLN cc_start: 0.9037 (mt0) cc_final: 0.8692 (mt0) REVERT: B 570 MET cc_start: 0.9104 (mtp) cc_final: 0.8788 (tpp) REVERT: B 586 TYR cc_start: 0.9178 (m-80) cc_final: 0.8930 (m-80) REVERT: B 589 SER cc_start: 0.9659 (t) cc_final: 0.9296 (p) REVERT: B 628 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8417 (mt-10) REVERT: B 686 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8296 (ttm-80) REVERT: C 109 PHE cc_start: 0.8292 (m-10) cc_final: 0.7841 (m-10) REVERT: C 137 MET cc_start: 0.7206 (mmt) cc_final: 0.6952 (mpp) REVERT: C 157 MET cc_start: 0.9318 (mtm) cc_final: 0.8989 (ptt) REVERT: C 174 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7224 (t80) REVERT: C 193 LEU cc_start: 0.7744 (mt) cc_final: 0.7521 (tt) REVERT: C 203 VAL cc_start: 0.8124 (t) cc_final: 0.7828 (t) REVERT: C 259 PHE cc_start: 0.7019 (t80) cc_final: 0.6743 (t80) REVERT: C 270 ASN cc_start: 0.8255 (m-40) cc_final: 0.7996 (t0) REVERT: D 95 MET cc_start: 0.8690 (tmm) cc_final: 0.8374 (tmm) REVERT: D 124 TRP cc_start: 0.8306 (t-100) cc_final: 0.8102 (t-100) REVERT: D 150 GLU cc_start: 0.5643 (tp30) cc_final: 0.5150 (mm-30) REVERT: D 242 TYR cc_start: 0.7853 (t80) cc_final: 0.7471 (t80) outliers start: 47 outliers final: 26 residues processed: 474 average time/residue: 0.1233 time to fit residues: 88.1899 Evaluate side-chains 456 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 424 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 100 optimal weight: 5.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097122 restraints weight = 25491.235| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.86 r_work: 0.2779 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16299 Z= 0.158 Angle : 0.611 11.764 22004 Z= 0.317 Chirality : 0.043 0.212 2348 Planarity : 0.004 0.054 2812 Dihedral : 6.541 62.740 2264 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.51 % Allowed : 22.05 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1928 helix: 1.31 (0.15), residues: 1140 sheet: -0.47 (0.40), residues: 158 loop : 0.38 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 225 TYR 0.023 0.001 TYR C 179 PHE 0.042 0.002 PHE D 227 TRP 0.021 0.002 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16298) covalent geometry : angle 0.61142 / 0.32 (22004) hydrogen bonds : bond 0.03764 / 2.41 ( 896) hydrogen bonds : angle 5.02811 / 3.56 ( 2616) Misc. bond : bond 0.00499 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 455 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8623 (m-70) cc_final: 0.8340 (m90) REVERT: A 104 TYR cc_start: 0.9369 (m-80) cc_final: 0.8899 (m-80) REVERT: A 173 LEU cc_start: 0.9721 (mt) cc_final: 0.9445 (mt) REVERT: A 178 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8795 (p) REVERT: A 266 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8834 (mtmm) REVERT: A 274 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8208 (ttm170) REVERT: A 286 ASP cc_start: 0.8787 (m-30) cc_final: 0.8403 (m-30) REVERT: A 334 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8688 (ptpt) REVERT: A 406 ASP cc_start: 0.8478 (m-30) cc_final: 0.8188 (m-30) REVERT: A 446 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8199 (mmm160) REVERT: B 31 GLU cc_start: 0.8958 (mp0) cc_final: 0.8434 (mp0) REVERT: B 75 GLU cc_start: 0.8501 (mp0) cc_final: 0.8123 (mp0) REVERT: B 79 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 181 ASP cc_start: 0.8803 (m-30) cc_final: 0.8138 (m-30) REVERT: B 211 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8045 (mm-30) REVERT: B 263 ASP cc_start: 0.8994 (m-30) cc_final: 0.8567 (m-30) REVERT: B 274 ARG cc_start: 0.8152 (ptp90) cc_final: 0.7081 (ptp-170) REVERT: B 276 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8861 (mmtt) REVERT: B 320 ASN cc_start: 0.8514 (m-40) cc_final: 0.8211 (m-40) REVERT: B 359 MET cc_start: 0.9435 (ttp) cc_final: 0.9136 (tmm) REVERT: B 570 MET cc_start: 0.9094 (mtp) cc_final: 0.8768 (tpp) REVERT: B 586 TYR cc_start: 0.9155 (m-80) cc_final: 0.8948 (m-80) REVERT: B 628 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8443 (mt-10) REVERT: B 686 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8285 (ttm-80) REVERT: C 137 MET cc_start: 0.7358 (mmt) cc_final: 0.7101 (mpp) REVERT: C 157 MET cc_start: 0.9335 (mtm) cc_final: 0.9073 (ptp) REVERT: C 174 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7195 (t80) REVERT: C 193 LEU cc_start: 0.7724 (mt) cc_final: 0.7512 (tt) REVERT: C 240 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7496 (mp) REVERT: C 259 PHE cc_start: 0.6910 (t80) cc_final: 0.6659 (t80) REVERT: D 95 MET cc_start: 0.8694 (tmm) cc_final: 0.8237 (tmm) REVERT: D 124 TRP cc_start: 0.8430 (t-100) cc_final: 0.8214 (t-100) REVERT: D 150 GLU cc_start: 0.5745 (tp30) cc_final: 0.5303 (mm-30) REVERT: D 196 ARG cc_start: 0.6461 (tmm-80) cc_final: 0.6229 (ptm-80) REVERT: D 227 PHE cc_start: 0.8367 (m-80) cc_final: 0.8070 (m-80) outliers start: 43 outliers final: 25 residues processed: 476 average time/residue: 0.1262 time to fit residues: 90.8890 Evaluate side-chains 456 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 426 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 20.0000 chunk 8 optimal weight: 0.0000 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 80 HIS ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.094693 restraints weight = 25704.587| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.87 r_work: 0.2739 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16299 Z= 0.227 Angle : 0.652 12.000 22004 Z= 0.340 Chirality : 0.045 0.201 2348 Planarity : 0.004 0.053 2812 Dihedral : 6.748 65.329 2264 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.51 % Allowed : 22.70 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1928 helix: 1.23 (0.15), residues: 1146 sheet: -0.50 (0.40), residues: 156 loop : 0.35 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 225 TYR 0.021 0.002 TYR D 162 PHE 0.037 0.002 PHE D 227 TRP 0.018 0.002 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (16298) covalent geometry : angle 0.65250 / 0.34 (22004) hydrogen bonds : bond 0.03950 / 2.55 ( 896) hydrogen bonds : angle 5.13033 / 3.64 ( 2616) Misc. bond : bond 0.00449 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 434 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.9446 (m-80) cc_final: 0.8816 (m-80) REVERT: A 178 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8880 (p) REVERT: A 266 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8855 (mtmm) REVERT: A 274 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8219 (ttm170) REVERT: A 286 ASP cc_start: 0.8741 (m-30) cc_final: 0.8377 (m-30) REVERT: A 334 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8683 (ptpt) REVERT: A 406 ASP cc_start: 0.8523 (m-30) cc_final: 0.8241 (m-30) REVERT: A 420 MET cc_start: 0.9348 (mmm) cc_final: 0.9059 (mmp) REVERT: A 446 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8228 (mmm160) REVERT: A 684 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 31 GLU cc_start: 0.8955 (mp0) cc_final: 0.8416 (mp0) REVERT: B 75 GLU cc_start: 0.8512 (mp0) cc_final: 0.8138 (mp0) REVERT: B 79 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 181 ASP cc_start: 0.8832 (m-30) cc_final: 0.8179 (m-30) REVERT: B 211 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 274 ARG cc_start: 0.8155 (ptp90) cc_final: 0.7050 (ptp-170) REVERT: B 276 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8882 (mmtt) REVERT: B 586 TYR cc_start: 0.9198 (m-80) cc_final: 0.8953 (m-80) REVERT: B 589 SER cc_start: 0.9638 (t) cc_final: 0.9282 (p) REVERT: B 628 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8488 (mt-10) REVERT: B 686 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8221 (ttm-80) REVERT: C 17 PHE cc_start: 0.8519 (p90) cc_final: 0.8223 (p90) REVERT: C 92 PHE cc_start: 0.7715 (t80) cc_final: 0.7510 (t80) REVERT: C 157 MET cc_start: 0.9339 (mtm) cc_final: 0.8967 (ptt) REVERT: C 178 PHE cc_start: 0.7506 (m-80) cc_final: 0.7120 (m-80) REVERT: C 240 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7306 (mp) REVERT: C 259 PHE cc_start: 0.6915 (t80) cc_final: 0.6666 (t80) REVERT: D 150 GLU cc_start: 0.5758 (tp30) cc_final: 0.5370 (mm-30) REVERT: D 242 TYR cc_start: 0.8031 (t80) cc_final: 0.7786 (t80) outliers start: 43 outliers final: 28 residues processed: 456 average time/residue: 0.1246 time to fit residues: 85.6733 Evaluate side-chains 436 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.097699 restraints weight = 25638.084| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.81 r_work: 0.2785 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16299 Z= 0.165 Angle : 0.656 11.436 22004 Z= 0.342 Chirality : 0.045 0.263 2348 Planarity : 0.004 0.053 2812 Dihedral : 6.734 64.134 2264 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.16 % Allowed : 23.10 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1928 helix: 1.20 (0.15), residues: 1139 sheet: -0.50 (0.40), residues: 156 loop : 0.27 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 196 TYR 0.026 0.001 TYR C 174 PHE 0.032 0.002 PHE C 259 TRP 0.020 0.002 TRP C 30 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (16298) covalent geometry : angle 0.65589 / 0.34 (22004) hydrogen bonds : bond 0.03923 / 2.53 ( 896) hydrogen bonds : angle 5.09336 / 3.61 ( 2616) Misc. bond : bond 0.00593 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 426 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.9384 (m-80) cc_final: 0.8821 (m-80) REVERT: A 178 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8933 (p) REVERT: A 184 ARG cc_start: 0.9217 (tpp-160) cc_final: 0.8989 (tpp-160) REVERT: A 266 LYS cc_start: 0.9049 (mtmm) cc_final: 0.8787 (mtmm) REVERT: A 274 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.8224 (ttm170) REVERT: A 286 ASP cc_start: 0.8698 (m-30) cc_final: 0.8346 (m-30) REVERT: A 334 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8645 (ptpt) REVERT: A 406 ASP cc_start: 0.8449 (m-30) cc_final: 0.8177 (m-30) REVERT: A 420 MET cc_start: 0.9354 (mmm) cc_final: 0.9128 (mmp) REVERT: A 446 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8310 (mmm160) REVERT: A 550 MET cc_start: 0.8705 (mtt) cc_final: 0.8346 (mtt) REVERT: A 655 THR cc_start: 0.9300 (m) cc_final: 0.9043 (t) REVERT: A 684 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7618 (t80) REVERT: B 31 GLU cc_start: 0.8964 (mp0) cc_final: 0.8425 (mp0) REVERT: B 56 ASP cc_start: 0.9038 (m-30) cc_final: 0.8639 (m-30) REVERT: B 75 GLU cc_start: 0.8512 (mp0) cc_final: 0.8131 (mp0) REVERT: B 79 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 147 GLN cc_start: 0.9225 (mt0) cc_final: 0.8872 (mm110) REVERT: B 181 ASP cc_start: 0.8819 (m-30) cc_final: 0.8200 (m-30) REVERT: B 184 ARG cc_start: 0.9249 (tpp-160) cc_final: 0.8956 (tpp80) REVERT: B 211 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7982 (mm-30) REVERT: B 263 ASP cc_start: 0.8974 (m-30) cc_final: 0.8543 (m-30) REVERT: B 274 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7066 (ptp-170) REVERT: B 276 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8859 (mmtt) REVERT: B 320 ASN cc_start: 0.8541 (m-40) cc_final: 0.8214 (m-40) REVERT: B 570 MET cc_start: 0.9055 (mtp) cc_final: 0.8720 (tpp) REVERT: B 589 SER cc_start: 0.9642 (t) cc_final: 0.9273 (p) REVERT: B 628 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8465 (mt-10) REVERT: B 686 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8237 (ttm-80) REVERT: C 17 PHE cc_start: 0.8506 (p90) cc_final: 0.8209 (p90) REVERT: C 137 MET cc_start: 0.6263 (mtt) cc_final: 0.5886 (mpp) REVERT: C 157 MET cc_start: 0.9208 (mtm) cc_final: 0.8859 (ptt) REVERT: D 95 MET cc_start: 0.8620 (tmm) cc_final: 0.8139 (tmm) REVERT: D 150 GLU cc_start: 0.5856 (tp30) cc_final: 0.5345 (mm-30) REVERT: D 246 LEU cc_start: 0.7146 (tp) cc_final: 0.6399 (tt) outliers start: 37 outliers final: 26 residues processed: 448 average time/residue: 0.1279 time to fit residues: 85.6355 Evaluate side-chains 451 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 421 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 174 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN C 192 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098095 restraints weight = 25801.870| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.95 r_work: 0.2810 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16299 Z= 0.149 Angle : 0.660 11.646 22004 Z= 0.343 Chirality : 0.044 0.256 2348 Planarity : 0.004 0.061 2812 Dihedral : 6.672 64.017 2264 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.93 % Allowed : 23.86 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1928 helix: 1.20 (0.15), residues: 1141 sheet: -0.41 (0.41), residues: 152 loop : 0.19 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.029 0.001 TYR C 179 PHE 0.047 0.002 PHE C 259 TRP 0.033 0.002 TRP D 44 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16298) covalent geometry : angle 0.65973 / 0.34 (22004) hydrogen bonds : bond 0.03881 / 2.52 ( 896) hydrogen bonds : angle 5.08218 / 3.60 ( 2616) Misc. bond : bond 0.00385 / 0.20 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 439 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8533 (m-70) cc_final: 0.8243 (m90) REVERT: A 104 TYR cc_start: 0.9326 (m-80) cc_final: 0.8935 (m-80) REVERT: A 178 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.8894 (p) REVERT: A 184 ARG cc_start: 0.9196 (tpp-160) cc_final: 0.8922 (tpp-160) REVERT: A 266 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8635 (mtmm) REVERT: A 274 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8184 (ttm-80) REVERT: A 286 ASP cc_start: 0.8685 (m-30) cc_final: 0.8332 (m-30) REVERT: A 406 ASP cc_start: 0.8434 (m-30) cc_final: 0.8152 (m-30) REVERT: A 446 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8551 (mmm160) REVERT: A 576 LEU cc_start: 0.9366 (mt) cc_final: 0.9135 (mt) REVERT: A 684 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 31 GLU cc_start: 0.8958 (mp0) cc_final: 0.8437 (mp0) REVERT: B 56 ASP cc_start: 0.9027 (m-30) cc_final: 0.8658 (m-30) REVERT: B 75 GLU cc_start: 0.8549 (mp0) cc_final: 0.8187 (mp0) REVERT: B 79 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8443 (mm-30) REVERT: B 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8946 (mm-40) REVERT: B 181 ASP cc_start: 0.8787 (m-30) cc_final: 0.8193 (m-30) REVERT: B 184 ARG cc_start: 0.9270 (tpp-160) cc_final: 0.8960 (tpp80) REVERT: B 274 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7101 (ptp-170) REVERT: B 276 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8825 (mmtt) REVERT: B 296 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8666 (mmmt) REVERT: B 320 ASN cc_start: 0.8569 (m-40) cc_final: 0.8280 (m-40) REVERT: B 359 MET cc_start: 0.9433 (ttp) cc_final: 0.9134 (tmm) REVERT: B 570 MET cc_start: 0.9060 (mtp) cc_final: 0.8722 (tpp) REVERT: B 586 TYR cc_start: 0.9194 (m-80) cc_final: 0.8992 (m-80) REVERT: B 589 SER cc_start: 0.9653 (t) cc_final: 0.9266 (p) REVERT: B 686 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8218 (ttm-80) REVERT: C 17 PHE cc_start: 0.8557 (p90) cc_final: 0.8298 (p90) REVERT: C 93 MET cc_start: 0.8776 (mtt) cc_final: 0.8379 (mtt) REVERT: C 181 GLN cc_start: 0.7672 (mp10) cc_final: 0.7289 (pm20) REVERT: C 230 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: C 240 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7580 (tp) REVERT: D 29 PHE cc_start: 0.3421 (t80) cc_final: 0.3139 (t80) REVERT: D 95 MET cc_start: 0.8473 (tmm) cc_final: 0.8010 (tmm) REVERT: D 150 GLU cc_start: 0.5846 (tp30) cc_final: 0.5573 (mm-30) REVERT: D 215 LYS cc_start: 0.7013 (mmtm) cc_final: 0.6266 (mmmt) REVERT: D 246 LEU cc_start: 0.7000 (tp) cc_final: 0.6442 (tt) outliers start: 33 outliers final: 22 residues processed: 459 average time/residue: 0.1227 time to fit residues: 84.5026 Evaluate side-chains 442 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 415 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 128 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 162 optimal weight: 0.0980 chunk 146 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100241 restraints weight = 25620.552| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.82 r_work: 0.2831 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16299 Z= 0.142 Angle : 0.676 16.018 22004 Z= 0.351 Chirality : 0.045 0.346 2348 Planarity : 0.004 0.061 2812 Dihedral : 6.624 64.266 2264 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.46 % Allowed : 24.85 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1928 helix: 1.17 (0.15), residues: 1140 sheet: -0.34 (0.41), residues: 152 loop : 0.20 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 686 TYR 0.028 0.001 TYR C 179 PHE 0.046 0.002 PHE D 172 TRP 0.047 0.003 TRP D 124 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16298) covalent geometry : angle 0.67573 / 0.35 (22004) hydrogen bonds : bond 0.03915 / 2.52 ( 896) hydrogen bonds : angle 5.09798 / 3.60 ( 2616) Misc. bond : bond 0.00300 / 0.16 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4379.09 seconds wall clock time: 76 minutes 9.61 seconds (4569.61 seconds total)