Starting phenix.real_space_refine on Fri Jul 3 19:28:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx8_44999/07_2026/9bx8_44999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx8_44999/07_2026/9bx8_44999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx8_44999/07_2026/9bx8_44999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx8_44999/07_2026/9bx8_44999.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx8_44999/07_2026/9bx8_44999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx8_44999/07_2026/9bx8_44999_neut.cif" } resolution = 3.59 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): 0.02s 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: 3.27, per 1000 atoms: 0.20 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 127.75, 133.882, 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: 1.13 Conformation dependent library (CDL) restraints added in 534.9 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: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.555A 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: 4.075A 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: 3.872A 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: 3.548A 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: 3.574A 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: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A 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: 6.888A 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: 7.139A 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: 3.736A 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: 5.890A 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: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A 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: 2.07 Time building geometry restraints manager: 1.50 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: 5014 1.34 - 1.46: 2987 1.46 - 1.58: 8122 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.91e+01 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 4.91e+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 2.37e+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 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 21471 2.12 - 4.24: 461 4.24 - 6.35: 57 6.35 - 8.47: 8 8.47 - 10.59: 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 2.00e+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=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.64 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8644 17.66 - 35.33: 853 35.33 - 52.99: 255 52.99 - 70.66: 64 70.66 - 88.32: 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 123.40 135.55 -12.15 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 -134.31 11.71 0 2.50e+00 1.60e-01 2.19e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2124 0.093 - 0.186: 186 0.186 - 0.279: 31 0.279 - 0.372: 5 0.372 - 0.465: 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 2.04 0.47 2.00e-01 2.50e+01 5.42e+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 2.95e+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 4.83e+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 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 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 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 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: 11874 3.11 - 3.70: 26443 3.70 - 4.30: 41240 4.30 - 4.90: 65005 Nonbonded interactions: 144694 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.918 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 1.966 3.060 ... (remaining 144689 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: 0.01 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.757 10.589 22004 Z= 0.462 Chirality : 0.059 0.465 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.904 88.322 6168 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 14.00 % 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 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.020 0.002 PHE C 227 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 0.75662 / 0.46 (22004) hydrogen bonds : bond 0.16169 / 10.52 ( 896) hydrogen bonds : angle 6.35333 / 4.48 ( 2616) Misc. bond : bond 0.83327 / 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 899 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 874 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: A 27 ASP cc_start: 0.7281 (p0) cc_final: 0.7071 (p0) REVERT: A 231 ASP cc_start: 0.8573 (t70) cc_final: 0.8362 (t70) REVERT: A 259 ASN cc_start: 0.7820 (m-40) cc_final: 0.7557 (m-40) REVERT: A 286 ASP cc_start: 0.7608 (m-30) cc_final: 0.6919 (m-30) REVERT: A 362 ASP cc_start: 0.6787 (m-30) cc_final: 0.6355 (m-30) REVERT: A 379 SER cc_start: 0.8842 (t) cc_final: 0.8402 (t) REVERT: A 591 THR cc_start: 0.8603 (p) cc_final: 0.8388 (m) REVERT: A 652 ILE cc_start: 0.9357 (mt) cc_final: 0.9058 (mt) REVERT: A 679 ILE cc_start: 0.9349 (mm) cc_final: 0.9122 (mm) REVERT: B 67 GLU cc_start: 0.7290 (mp0) cc_final: 0.7082 (mp0) REVERT: B 155 THR cc_start: 0.9148 (m) cc_final: 0.8840 (t) REVERT: B 177 ASP cc_start: 0.8411 (t0) cc_final: 0.8193 (t0) REVERT: B 194 LYS cc_start: 0.8972 (tttt) cc_final: 0.8722 (ttpt) REVERT: B 211 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6997 (mm-30) REVERT: B 250 TYR cc_start: 0.8678 (m-80) cc_final: 0.7882 (m-80) REVERT: B 286 ASP cc_start: 0.7187 (m-30) cc_final: 0.6427 (m-30) REVERT: B 357 TYR cc_start: 0.8718 (m-10) cc_final: 0.8350 (m-80) REVERT: B 362 ASP cc_start: 0.7219 (m-30) cc_final: 0.6461 (m-30) REVERT: B 379 SER cc_start: 0.9080 (t) cc_final: 0.8198 (t) REVERT: B 456 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8478 (ttpp) REVERT: B 598 MET cc_start: 0.7652 (mtm) cc_final: 0.7064 (mtm) REVERT: B 628 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 66 ASP cc_start: 0.5021 (m-30) cc_final: 0.4480 (m-30) REVERT: C 92 PHE cc_start: 0.7840 (t80) cc_final: 0.7531 (t80) REVERT: C 131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6462 (mt) REVERT: D 178 PHE cc_start: 0.5738 (m-80) cc_final: 0.5174 (m-80) REVERT: D 213 TYR cc_start: 0.4890 (t80) cc_final: 0.4633 (t80) REVERT: D 260 ILE cc_start: 0.7299 (mt) cc_final: 0.6411 (mp) REVERT: D 321 TYR cc_start: 0.7759 (m-80) cc_final: 0.6592 (m-80) outliers start: 25 outliers final: 4 residues processed: 882 average time/residue: 0.1140 time to fit residues: 147.6535 Evaluate side-chains 633 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 628 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0270 overall best weight: 0.4640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 14 ASN A 19 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 312 GLN A 370 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 588 GLN B 646 GLN C 24 GLN C 28 GLN C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 91 ASN D 127 GLN D 136 GLN D 233 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104382 restraints weight = 28368.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108300 restraints weight = 11879.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110756 restraints weight = 6810.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112158 restraints weight = 4745.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113168 restraints weight = 3816.603| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16299 Z= 0.151 Angle : 0.644 10.323 22004 Z= 0.346 Chirality : 0.044 0.206 2348 Planarity : 0.004 0.057 2812 Dihedral : 7.038 63.018 2270 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.56 % Allowed : 17.91 % Favored : 78.53 % 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: 1.54 (0.18), residues: 1928 helix: 1.45 (0.15), residues: 1125 sheet: 1.43 (0.43), residues: 96 loop : 0.44 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.030 0.002 TYR C 173 PHE 0.031 0.002 PHE B 261 TRP 0.029 0.003 TRP C 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16298) covalent geometry : angle 0.64442 / 0.35 (22004) hydrogen bonds : bond 0.04777 / 3.00 ( 896) hydrogen bonds : angle 5.21665 / 3.62 ( 2616) Misc. bond : bond 0.00003 / 0.00 ( 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 756 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 695 time to evaluate : 0.625 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: A 246 SER cc_start: 0.7301 (m) cc_final: 0.6749 (p) REVERT: A 286 ASP cc_start: 0.8704 (m-30) cc_final: 0.7507 (m-30) REVERT: A 312 GLN cc_start: 0.8658 (pt0) cc_final: 0.8412 (pt0) REVERT: A 344 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 362 ASP cc_start: 0.7532 (m-30) cc_final: 0.6762 (m-30) REVERT: A 379 SER cc_start: 0.9128 (t) cc_final: 0.8824 (t) REVERT: A 535 ASP cc_start: 0.8190 (t0) cc_final: 0.7796 (t0) REVERT: A 602 GLU cc_start: 0.8027 (tt0) cc_final: 0.7812 (tt0) REVERT: B 109 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8702 (m-40) REVERT: B 250 TYR cc_start: 0.9278 (m-80) cc_final: 0.7961 (m-80) REVERT: B 286 ASP cc_start: 0.8031 (m-30) cc_final: 0.7149 (m-30) REVERT: B 321 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 334 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8695 (ptpp) REVERT: B 355 TYR cc_start: 0.8714 (m-80) cc_final: 0.8436 (m-80) REVERT: B 357 TYR cc_start: 0.9028 (m-10) cc_final: 0.8567 (m-80) REVERT: B 362 ASP cc_start: 0.7833 (m-30) cc_final: 0.6660 (m-30) REVERT: B 379 SER cc_start: 0.9292 (t) cc_final: 0.8372 (t) REVERT: B 586 TYR cc_start: 0.8704 (m-80) cc_final: 0.8452 (m-80) REVERT: B 598 MET cc_start: 0.8241 (mtm) cc_final: 0.7628 (mtp) REVERT: B 599 GLU cc_start: 0.8269 (pm20) cc_final: 0.7797 (pm20) REVERT: B 604 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8080 (tpp80) REVERT: B 628 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7644 (mm-30) REVERT: C 21 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8217 (t80) REVERT: C 25 ASN cc_start: 0.8486 (m-40) cc_final: 0.8098 (m-40) REVERT: C 42 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7523 (pp) REVERT: C 95 MET cc_start: 0.8476 (tmm) cc_final: 0.8195 (tmm) REVERT: C 122 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: C 183 LYS cc_start: 0.8117 (pttt) cc_final: 0.7888 (pttp) REVERT: C 213 TYR cc_start: 0.7658 (t80) cc_final: 0.7381 (t80) REVERT: C 242 TYR cc_start: 0.8929 (t80) cc_final: 0.8551 (t80) REVERT: C 260 ILE cc_start: 0.8135 (pt) cc_final: 0.7847 (pt) REVERT: C 269 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (ppp) REVERT: C 283 ASN cc_start: 0.7483 (p0) cc_final: 0.7201 (p0) REVERT: C 287 LEU cc_start: 0.0908 (OUTLIER) cc_final: 0.0706 (mp) REVERT: D 17 PHE cc_start: 0.5800 (m-80) cc_final: 0.5264 (m-80) REVERT: D 42 LEU cc_start: 0.8783 (tp) cc_final: 0.8487 (mp) REVERT: D 117 THR cc_start: 0.8875 (m) cc_final: 0.7827 (m) REVERT: D 137 MET cc_start: 0.4439 (mtp) cc_final: 0.3903 (mmm) REVERT: D 154 PHE cc_start: 0.9255 (t80) cc_final: 0.8721 (t80) REVERT: D 157 MET cc_start: 0.9130 (mtp) cc_final: 0.8770 (ptp) REVERT: D 169 TYR cc_start: 0.8083 (m-80) cc_final: 0.7641 (m-80) REVERT: D 213 TYR cc_start: 0.8020 (t80) cc_final: 0.7607 (t80) REVERT: D 215 LYS cc_start: 0.8865 (mtmp) cc_final: 0.8651 (mtmm) REVERT: D 244 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7757 (pt0) outliers start: 61 outliers final: 17 residues processed: 716 average time/residue: 0.1191 time to fit residues: 128.6135 Evaluate side-chains 605 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 581 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 646 GLN Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 370 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 370 ASN B 475 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 192 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN D 127 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093689 restraints weight = 29116.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097289 restraints weight = 12099.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099530 restraints weight = 6940.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100885 restraints weight = 4848.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101650 restraints weight = 3880.605| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16299 Z= 0.196 Angle : 0.626 8.461 22004 Z= 0.338 Chirality : 0.044 0.158 2348 Planarity : 0.004 0.054 2812 Dihedral : 6.976 62.373 2267 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.50 % Allowed : 19.54 % Favored : 76.95 % 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: 1.40 (0.19), residues: 1928 helix: 1.38 (0.15), residues: 1126 sheet: 0.12 (0.40), residues: 144 loop : 0.54 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.023 0.002 TYR C 236 PHE 0.036 0.002 PHE D 172 TRP 0.024 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (16298) covalent geometry : angle 0.62588 / 0.34 (22004) hydrogen bonds : bond 0.04341 / 2.72 ( 896) hydrogen bonds : angle 5.10346 / 3.56 ( 2616) Misc. bond : bond 0.00116 / 0.06 ( 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 678 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 618 time to evaluate : 0.639 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: A 150 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8424 (tp-100) REVERT: A 156 PHE cc_start: 0.9131 (t80) cc_final: 0.8915 (t80) REVERT: A 246 SER cc_start: 0.7168 (m) cc_final: 0.6600 (p) REVERT: A 266 LYS cc_start: 0.9031 (mttt) cc_final: 0.8810 (mttt) REVERT: A 275 VAL cc_start: 0.9513 (t) cc_final: 0.9307 (t) REVERT: A 286 ASP cc_start: 0.8749 (m-30) cc_final: 0.7667 (m-30) REVERT: A 344 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 355 TYR cc_start: 0.8954 (m-80) cc_final: 0.8707 (m-10) REVERT: A 362 ASP cc_start: 0.7858 (m-30) cc_final: 0.6742 (m-30) REVERT: A 379 SER cc_start: 0.9069 (t) cc_final: 0.8840 (t) REVERT: A 444 ASP cc_start: 0.8411 (t70) cc_final: 0.7945 (t0) REVERT: A 485 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: B 98 PHE cc_start: 0.9355 (t80) cc_final: 0.8856 (t80) REVERT: B 109 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8920 (m-40) REVERT: B 250 TYR cc_start: 0.9391 (m-80) cc_final: 0.7721 (m-80) REVERT: B 263 ASP cc_start: 0.8747 (m-30) cc_final: 0.8388 (m-30) REVERT: B 286 ASP cc_start: 0.8207 (m-30) cc_final: 0.7221 (m-30) REVERT: B 318 ASP cc_start: 0.8511 (t0) cc_final: 0.7736 (t0) REVERT: B 355 TYR cc_start: 0.8804 (m-80) cc_final: 0.8503 (m-80) REVERT: B 362 ASP cc_start: 0.8150 (m-30) cc_final: 0.6973 (m-30) REVERT: B 379 SER cc_start: 0.9128 (t) cc_final: 0.8350 (t) REVERT: B 402 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 416 ILE cc_start: 0.9492 (mt) cc_final: 0.9290 (mt) REVERT: B 417 LEU cc_start: 0.9254 (tt) cc_final: 0.8968 (tt) REVERT: B 466 MET cc_start: 0.8768 (ptm) cc_final: 0.8362 (ptm) REVERT: B 493 MET cc_start: 0.9508 (tmm) cc_final: 0.9111 (tmm) REVERT: B 586 TYR cc_start: 0.9229 (m-80) cc_final: 0.8501 (m-80) REVERT: B 599 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: B 602 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 603 GLU cc_start: 0.8206 (tp30) cc_final: 0.7558 (tp30) REVERT: B 612 TYR cc_start: 0.8627 (m-80) cc_final: 0.6863 (m-80) REVERT: B 628 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7856 (mt-10) REVERT: B 650 GLN cc_start: 0.8469 (mt0) cc_final: 0.8255 (mt0) REVERT: C 20 MET cc_start: 0.8090 (tpt) cc_final: 0.7588 (ptt) REVERT: C 21 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8194 (t80) REVERT: C 25 ASN cc_start: 0.8729 (m-40) cc_final: 0.8087 (m-40) REVERT: C 37 LEU cc_start: 0.6013 (mp) cc_final: 0.5206 (mt) REVERT: C 42 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7785 (pp) REVERT: C 92 PHE cc_start: 0.8320 (t80) cc_final: 0.7817 (t80) REVERT: C 95 MET cc_start: 0.8461 (tmm) cc_final: 0.7997 (tmm) REVERT: C 105 TYR cc_start: 0.7796 (m-80) cc_final: 0.7488 (m-80) REVERT: C 122 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: C 145 ILE cc_start: 0.8638 (tp) cc_final: 0.8262 (tp) REVERT: C 178 PHE cc_start: 0.9258 (m-10) cc_final: 0.8770 (m-10) REVERT: C 183 LYS cc_start: 0.7823 (pttt) cc_final: 0.7495 (pttm) REVERT: C 227 PHE cc_start: 0.8644 (t80) cc_final: 0.8290 (t80) REVERT: C 242 TYR cc_start: 0.9017 (t80) cc_final: 0.8597 (t80) REVERT: C 260 ILE cc_start: 0.8445 (pt) cc_final: 0.8006 (pt) REVERT: D 42 LEU cc_start: 0.8699 (tp) cc_final: 0.8271 (mp) REVERT: D 46 TYR cc_start: 0.8884 (m-10) cc_final: 0.8389 (m-10) REVERT: D 137 MET cc_start: 0.5078 (mtp) cc_final: 0.4644 (mmt) REVERT: D 154 PHE cc_start: 0.9320 (t80) cc_final: 0.8741 (t80) REVERT: D 169 TYR cc_start: 0.8236 (m-80) cc_final: 0.7875 (m-80) REVERT: D 178 PHE cc_start: 0.9050 (m-80) cc_final: 0.8561 (m-80) REVERT: D 186 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8354 (mp10) REVERT: D 213 TYR cc_start: 0.8364 (t80) cc_final: 0.7752 (t80) REVERT: D 233 ASN cc_start: 0.8185 (m-40) cc_final: 0.7957 (m110) REVERT: D 242 TYR cc_start: 0.7964 (t80) cc_final: 0.7509 (t80) REVERT: D 244 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8015 (pt0) outliers start: 60 outliers final: 39 residues processed: 647 average time/residue: 0.1301 time to fit residues: 125.9341 Evaluate side-chains 602 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 558 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 668 ASN B 44 ASN B 131 ASN B 202 ASN B 304 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093685 restraints weight = 29099.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097225 restraints weight = 12237.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.099367 restraints weight = 7131.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100581 restraints weight = 5066.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.101329 restraints weight = 4143.578| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16299 Z= 0.249 Angle : 0.659 14.499 22004 Z= 0.349 Chirality : 0.045 0.175 2348 Planarity : 0.004 0.055 2812 Dihedral : 7.098 63.767 2266 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.08 % Allowed : 21.24 % Favored : 74.68 % 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: 1.16 (0.19), residues: 1928 helix: 1.19 (0.15), residues: 1144 sheet: -0.20 (0.40), residues: 152 loop : 0.47 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.025 0.002 TYR D 236 PHE 0.030 0.002 PHE D 172 TRP 0.025 0.003 TRP C 30 HIS 0.005 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (16298) covalent geometry : angle 0.65858 / 0.35 (22004) hydrogen bonds : bond 0.04220 / 2.66 ( 896) hydrogen bonds : angle 5.15988 / 3.62 ( 2616) Misc. bond : bond 0.00091 / 0.05 ( 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 645 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 575 time to evaluate : 0.563 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: A 150 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8523 (tp-100) REVERT: A 228 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8766 (mmtt) REVERT: A 266 LYS cc_start: 0.9078 (mttt) cc_final: 0.8859 (mttt) REVERT: A 286 ASP cc_start: 0.8636 (m-30) cc_final: 0.7698 (m-30) REVERT: A 344 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 345 LYS cc_start: 0.9187 (tptm) cc_final: 0.8975 (tttp) REVERT: A 362 ASP cc_start: 0.7799 (m-30) cc_final: 0.6697 (m-30) REVERT: A 379 SER cc_start: 0.9055 (t) cc_final: 0.8815 (t) REVERT: A 384 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6227 (pm20) REVERT: A 485 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8081 (mtm-85) REVERT: A 684 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: B 98 PHE cc_start: 0.9349 (t80) cc_final: 0.8762 (t80) REVERT: B 109 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8666 (m-40) REVERT: B 250 TYR cc_start: 0.9416 (m-80) cc_final: 0.7396 (m-80) REVERT: B 263 ASP cc_start: 0.8684 (m-30) cc_final: 0.8350 (m-30) REVERT: B 286 ASP cc_start: 0.8027 (m-30) cc_final: 0.7304 (m-30) REVERT: B 317 MET cc_start: 0.8563 (mtp) cc_final: 0.8285 (mtp) REVERT: B 355 TYR cc_start: 0.8841 (m-80) cc_final: 0.8519 (m-80) REVERT: B 362 ASP cc_start: 0.8113 (m-30) cc_final: 0.6808 (m-30) REVERT: B 379 SER cc_start: 0.9139 (t) cc_final: 0.8332 (t) REVERT: B 586 TYR cc_start: 0.9141 (m-80) cc_final: 0.8525 (m-80) REVERT: B 599 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: B 602 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 603 GLU cc_start: 0.8186 (tp30) cc_final: 0.7706 (tp30) REVERT: B 604 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8148 (tpp80) REVERT: B 612 TYR cc_start: 0.8771 (m-80) cc_final: 0.7311 (m-80) REVERT: B 628 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 20 MET cc_start: 0.8183 (tpt) cc_final: 0.7766 (ptt) REVERT: C 21 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8306 (t80) REVERT: C 40 ASP cc_start: 0.8369 (p0) cc_final: 0.8008 (p0) REVERT: C 42 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7742 (pp) REVERT: C 92 PHE cc_start: 0.8374 (t80) cc_final: 0.8158 (t80) REVERT: C 95 MET cc_start: 0.8620 (tmm) cc_final: 0.8328 (tmm) REVERT: C 122 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8034 (m-10) REVERT: C 149 ASP cc_start: 0.8587 (t0) cc_final: 0.8346 (t0) REVERT: C 227 PHE cc_start: 0.8733 (t80) cc_final: 0.8429 (t80) REVERT: C 229 ILE cc_start: 0.7511 (mm) cc_final: 0.7294 (mm) REVERT: C 242 TYR cc_start: 0.9025 (t80) cc_final: 0.8723 (t80) REVERT: C 256 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7857 (m) REVERT: C 270 ASN cc_start: 0.8623 (m-40) cc_final: 0.8397 (m-40) REVERT: C 287 LEU cc_start: 0.1705 (OUTLIER) cc_final: 0.1341 (mt) REVERT: D 17 PHE cc_start: 0.5634 (m-80) cc_final: 0.5182 (m-80) REVERT: D 46 TYR cc_start: 0.8975 (m-10) cc_final: 0.8686 (m-10) REVERT: D 56 MET cc_start: 0.7241 (mmm) cc_final: 0.6801 (ptp) REVERT: D 137 MET cc_start: 0.5863 (mtp) cc_final: 0.5425 (mmt) REVERT: D 154 PHE cc_start: 0.9274 (t80) cc_final: 0.8731 (t80) REVERT: D 186 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8273 (mp10) REVERT: D 213 TYR cc_start: 0.8544 (t80) cc_final: 0.8089 (t80) REVERT: D 263 ASN cc_start: 0.8604 (p0) cc_final: 0.8206 (p0) REVERT: D 287 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4433 (mp) outliers start: 70 outliers final: 45 residues processed: 606 average time/residue: 0.1266 time to fit residues: 114.9826 Evaluate side-chains 593 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 538 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 131 ASN B 568 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 28 GLN D 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.097964 restraints weight = 28883.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101520 restraints weight = 12084.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.103738 restraints weight = 6963.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104934 restraints weight = 4916.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105701 restraints weight = 4018.443| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16299 Z= 0.147 Angle : 0.621 12.317 22004 Z= 0.328 Chirality : 0.043 0.179 2348 Planarity : 0.003 0.053 2812 Dihedral : 6.813 59.809 2264 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.56 % Allowed : 23.69 % Favored : 72.75 % 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: 1.13 (0.19), residues: 1928 helix: 1.19 (0.15), residues: 1148 sheet: -0.35 (0.40), residues: 152 loop : 0.45 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.023 0.001 TYR D 236 PHE 0.030 0.002 PHE D 172 TRP 0.020 0.002 TRP C 124 HIS 0.008 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16298) covalent geometry : angle 0.62105 / 0.33 (22004) hydrogen bonds : bond 0.03923 / 2.50 ( 896) hydrogen bonds : angle 5.05236 / 3.54 ( 2616) Misc. bond : bond 0.00086 / 0.05 ( 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 648 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 587 time to evaluate : 0.635 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 102 ASN cc_start: 0.8817 (m-40) cc_final: 0.8496 (t0) REVERT: A 150 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8467 (tp-100) REVERT: A 228 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8745 (mmtt) REVERT: A 266 LYS cc_start: 0.9043 (mttt) cc_final: 0.8793 (mttt) REVERT: A 286 ASP cc_start: 0.8652 (m-30) cc_final: 0.7765 (m-30) REVERT: A 322 MET cc_start: 0.8039 (mmt) cc_final: 0.7760 (tpp) REVERT: A 344 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 345 LYS cc_start: 0.9134 (tptm) cc_final: 0.8836 (tttp) REVERT: A 355 TYR cc_start: 0.8892 (m-80) cc_final: 0.8451 (m-80) REVERT: A 362 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: A 379 SER cc_start: 0.9079 (t) cc_final: 0.8873 (t) REVERT: A 485 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8035 (mtm-85) REVERT: A 570 MET cc_start: 0.8756 (mtp) cc_final: 0.8482 (mtp) REVERT: A 602 GLU cc_start: 0.7750 (tt0) cc_final: 0.7463 (tt0) REVERT: A 603 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 639 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: A 684 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: A 688 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7127 (pptt) REVERT: B 98 PHE cc_start: 0.9254 (t80) cc_final: 0.8573 (t80) REVERT: B 109 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: B 250 TYR cc_start: 0.9368 (m-80) cc_final: 0.7436 (m-80) REVERT: B 263 ASP cc_start: 0.8612 (m-30) cc_final: 0.8268 (m-30) REVERT: B 286 ASP cc_start: 0.8056 (m-30) cc_final: 0.7468 (m-30) REVERT: B 317 MET cc_start: 0.8489 (mtp) cc_final: 0.8280 (mtp) REVERT: B 355 TYR cc_start: 0.8677 (m-80) cc_final: 0.8383 (m-80) REVERT: B 357 TYR cc_start: 0.8906 (m-10) cc_final: 0.8629 (m-80) REVERT: B 362 ASP cc_start: 0.7994 (m-30) cc_final: 0.6547 (m-30) REVERT: B 379 SER cc_start: 0.9122 (t) cc_final: 0.8235 (t) REVERT: B 402 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7952 (tm-30) REVERT: B 416 ILE cc_start: 0.9548 (mt) cc_final: 0.9316 (mt) REVERT: B 466 MET cc_start: 0.8830 (ptm) cc_final: 0.8525 (ptp) REVERT: B 586 TYR cc_start: 0.9143 (m-80) cc_final: 0.8604 (m-80) REVERT: B 599 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 602 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 610 LYS cc_start: 0.8453 (tppt) cc_final: 0.7061 (tppt) REVERT: B 612 TYR cc_start: 0.8519 (m-80) cc_final: 0.7831 (m-80) REVERT: B 628 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7894 (mt-10) REVERT: C 20 MET cc_start: 0.8121 (tpt) cc_final: 0.7678 (ptp) REVERT: C 21 PHE cc_start: 0.8902 (m-80) cc_final: 0.8209 (t80) REVERT: C 44 TRP cc_start: 0.7729 (t-100) cc_final: 0.7497 (t-100) REVERT: C 82 ASP cc_start: 0.8507 (m-30) cc_final: 0.7850 (p0) REVERT: C 122 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8080 (m-10) REVERT: C 183 LYS cc_start: 0.7990 (pttt) cc_final: 0.7775 (pttp) REVERT: C 227 PHE cc_start: 0.8741 (t80) cc_final: 0.8459 (t80) REVERT: C 242 TYR cc_start: 0.9240 (t80) cc_final: 0.8740 (t80) REVERT: C 261 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8023 (mtm180) REVERT: C 270 ASN cc_start: 0.8728 (m-40) cc_final: 0.8478 (m-40) REVERT: D 27 LYS cc_start: 0.8890 (mttt) cc_final: 0.8661 (pttp) REVERT: D 46 TYR cc_start: 0.8962 (m-10) cc_final: 0.8634 (m-10) REVERT: D 137 MET cc_start: 0.6077 (mtp) cc_final: 0.5726 (mmt) REVERT: D 154 PHE cc_start: 0.9321 (t80) cc_final: 0.8829 (t80) REVERT: D 178 PHE cc_start: 0.9176 (m-80) cc_final: 0.8840 (m-80) REVERT: D 186 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8328 (mp10) REVERT: D 213 TYR cc_start: 0.8966 (t80) cc_final: 0.8295 (t80) REVERT: D 224 LEU cc_start: 0.9227 (pp) cc_final: 0.8977 (pp) REVERT: D 227 PHE cc_start: 0.9266 (m-80) cc_final: 0.8984 (m-80) REVERT: D 242 TYR cc_start: 0.8154 (t80) cc_final: 0.7879 (t80) REVERT: D 263 ASN cc_start: 0.8597 (p0) cc_final: 0.8148 (p0) outliers start: 61 outliers final: 35 residues processed: 606 average time/residue: 0.1292 time to fit residues: 118.0240 Evaluate side-chains 580 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 538 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 282 ILE 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: 3.9990 chunk 4 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 202 ASN B 668 ASN C 24 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.141517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099907 restraints weight = 28696.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103354 restraints weight = 11885.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105517 restraints weight = 7006.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106836 restraints weight = 4942.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107602 restraints weight = 3986.878| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16299 Z= 0.138 Angle : 0.627 11.928 22004 Z= 0.330 Chirality : 0.043 0.203 2348 Planarity : 0.004 0.051 2812 Dihedral : 6.718 59.961 2264 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.80 % Allowed : 25.32 % Favored : 71.88 % 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: 1.08 (0.19), residues: 1928 helix: 1.15 (0.15), residues: 1146 sheet: -0.47 (0.40), residues: 152 loop : 0.45 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 225 TYR 0.025 0.001 TYR C 142 PHE 0.028 0.002 PHE D 172 TRP 0.023 0.002 TRP C 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16298) covalent geometry : angle 0.62677 / 0.33 (22004) hydrogen bonds : bond 0.03837 / 2.46 ( 896) hydrogen bonds : angle 5.06322 / 3.55 ( 2616) Misc. bond : bond 0.00073 / 0.04 ( 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 629 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 581 time to evaluate : 0.626 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 102 ASN cc_start: 0.8855 (m-40) cc_final: 0.8500 (t0) REVERT: A 144 MET cc_start: 0.8541 (mtm) cc_final: 0.7872 (mtm) REVERT: A 266 LYS cc_start: 0.9004 (mttt) cc_final: 0.8716 (mttt) REVERT: A 286 ASP cc_start: 0.8637 (m-30) cc_final: 0.7733 (m-30) REVERT: A 322 MET cc_start: 0.8026 (mmt) cc_final: 0.7746 (tpp) REVERT: A 344 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 345 LYS cc_start: 0.9112 (tptm) cc_final: 0.8894 (tttp) REVERT: A 355 TYR cc_start: 0.8864 (m-80) cc_final: 0.8415 (m-80) REVERT: A 362 ASP cc_start: 0.7643 (m-30) cc_final: 0.6621 (m-30) REVERT: A 379 SER cc_start: 0.9109 (t) cc_final: 0.8880 (t) REVERT: A 485 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.7940 (mtm-85) REVERT: A 493 MET cc_start: 0.9071 (tmm) cc_final: 0.8819 (tmm) REVERT: A 570 MET cc_start: 0.8760 (mtp) cc_final: 0.8481 (mtp) REVERT: A 586 TYR cc_start: 0.8941 (m-10) cc_final: 0.8428 (m-10) REVERT: A 602 GLU cc_start: 0.7933 (tt0) cc_final: 0.6935 (tt0) REVERT: A 639 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: A 684 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: A 688 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7107 (pptt) REVERT: B 98 PHE cc_start: 0.9243 (t80) cc_final: 0.8511 (t80) REVERT: B 109 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8394 (m-40) REVERT: B 250 TYR cc_start: 0.9348 (m-80) cc_final: 0.7475 (m-80) REVERT: B 263 ASP cc_start: 0.8624 (m-30) cc_final: 0.8286 (m-30) REVERT: B 286 ASP cc_start: 0.8038 (m-30) cc_final: 0.7313 (m-30) REVERT: B 317 MET cc_start: 0.8401 (mtp) cc_final: 0.7553 (mtp) REVERT: B 355 TYR cc_start: 0.8602 (m-80) cc_final: 0.8318 (m-80) REVERT: B 357 TYR cc_start: 0.8897 (m-10) cc_final: 0.8611 (m-80) REVERT: B 362 ASP cc_start: 0.8015 (m-30) cc_final: 0.6548 (m-30) REVERT: B 379 SER cc_start: 0.9118 (t) cc_final: 0.8295 (t) REVERT: B 466 MET cc_start: 0.8721 (ptm) cc_final: 0.8448 (ptp) REVERT: B 586 TYR cc_start: 0.9177 (m-80) cc_final: 0.8624 (m-80) REVERT: B 599 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: B 602 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 612 TYR cc_start: 0.8526 (m-80) cc_final: 0.7956 (m-80) REVERT: B 615 MET cc_start: 0.9276 (mmm) cc_final: 0.8621 (mmp) REVERT: B 628 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7931 (mt-10) REVERT: C 20 MET cc_start: 0.7990 (tpt) cc_final: 0.7164 (ptp) REVERT: C 21 PHE cc_start: 0.8886 (m-80) cc_final: 0.8221 (t80) REVERT: C 92 PHE cc_start: 0.8007 (t80) cc_final: 0.7801 (t80) REVERT: C 122 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: C 134 LYS cc_start: 0.9374 (pttt) cc_final: 0.8966 (tppt) REVERT: C 149 ASP cc_start: 0.8630 (t0) cc_final: 0.8381 (t0) REVERT: C 174 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7233 (t80) REVERT: C 183 LYS cc_start: 0.7946 (pttt) cc_final: 0.7716 (pttp) REVERT: C 192 ASN cc_start: 0.8856 (p0) cc_final: 0.8536 (p0) REVERT: C 242 TYR cc_start: 0.9235 (t80) cc_final: 0.8782 (t80) REVERT: C 270 ASN cc_start: 0.8783 (m-40) cc_final: 0.8536 (m-40) REVERT: C 276 TYR cc_start: 0.7979 (t80) cc_final: 0.7614 (t80) REVERT: C 318 ASP cc_start: 0.9019 (m-30) cc_final: 0.8757 (m-30) REVERT: D 42 LEU cc_start: 0.8750 (tp) cc_final: 0.8453 (tp) REVERT: D 46 TYR cc_start: 0.9015 (m-10) cc_final: 0.8706 (m-10) REVERT: D 56 MET cc_start: 0.6860 (mmm) cc_final: 0.6036 (ptp) REVERT: D 96 MET cc_start: 0.7313 (mmt) cc_final: 0.7103 (mmt) REVERT: D 131 LEU cc_start: 0.8009 (tp) cc_final: 0.7808 (tt) REVERT: D 137 MET cc_start: 0.6257 (mtp) cc_final: 0.5820 (mmt) REVERT: D 154 PHE cc_start: 0.9300 (t80) cc_final: 0.8877 (t80) REVERT: D 169 TYR cc_start: 0.8601 (m-80) cc_final: 0.8143 (m-80) REVERT: D 186 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8280 (mp10) REVERT: D 213 TYR cc_start: 0.9058 (t80) cc_final: 0.8728 (t80) REVERT: D 263 ASN cc_start: 0.8529 (p0) cc_final: 0.8069 (p0) outliers start: 48 outliers final: 32 residues processed: 596 average time/residue: 0.1285 time to fit residues: 114.3197 Evaluate side-chains 576 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 537 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 668 ASN C 24 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3750 r_free = 0.3750 target = 0.140722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098924 restraints weight = 28609.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102487 restraints weight = 11786.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104627 restraints weight = 6805.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105831 restraints weight = 4841.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106585 restraints weight = 3982.906| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5983 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= 0.143 Angle : 0.647 11.653 22004 Z= 0.339 Chirality : 0.044 0.205 2348 Planarity : 0.004 0.050 2812 Dihedral : 6.676 60.566 2264 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.15 % Allowed : 26.43 % Favored : 70.42 % 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: 1.03 (0.19), residues: 1928 helix: 1.10 (0.15), residues: 1144 sheet: -0.48 (0.40), residues: 154 loop : 0.46 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 225 TYR 0.024 0.001 TYR C 142 PHE 0.034 0.002 PHE D 227 TRP 0.024 0.002 TRP C 124 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16298) covalent geometry : angle 0.64653 / 0.34 (22004) hydrogen bonds : bond 0.03857 / 2.43 ( 896) hydrogen bonds : angle 5.13176 / 3.61 ( 2616) Misc. bond : bond 0.00065 / 0.03 ( 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 615 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 561 time to evaluate : 0.677 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 102 ASN cc_start: 0.8843 (m-40) cc_final: 0.8423 (t0) REVERT: A 228 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8714 (mmtt) REVERT: A 266 LYS cc_start: 0.8948 (mttt) cc_final: 0.8650 (mttt) REVERT: A 286 ASP cc_start: 0.8641 (m-30) cc_final: 0.7761 (m-30) REVERT: A 322 MET cc_start: 0.8003 (mmt) cc_final: 0.7733 (tpp) REVERT: A 344 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 345 LYS cc_start: 0.9122 (tptm) cc_final: 0.8869 (tttp) REVERT: A 355 TYR cc_start: 0.8863 (m-80) cc_final: 0.8425 (m-80) REVERT: A 362 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: A 485 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.7655 (mtm110) REVERT: A 570 MET cc_start: 0.8759 (mtp) cc_final: 0.8458 (mtp) REVERT: A 586 TYR cc_start: 0.8958 (m-10) cc_final: 0.8584 (m-10) REVERT: A 639 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: A 684 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: B 15 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8076 (mp0) REVERT: B 98 PHE cc_start: 0.9260 (t80) cc_final: 0.8547 (t80) REVERT: B 121 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8821 (tpt170) REVERT: B 250 TYR cc_start: 0.9353 (m-80) cc_final: 0.7477 (m-80) REVERT: B 263 ASP cc_start: 0.8622 (m-30) cc_final: 0.8266 (m-30) REVERT: B 286 ASP cc_start: 0.7982 (m-30) cc_final: 0.7231 (m-30) REVERT: B 317 MET cc_start: 0.8390 (mtp) cc_final: 0.7562 (mtp) REVERT: B 355 TYR cc_start: 0.8590 (m-80) cc_final: 0.8350 (m-80) REVERT: B 357 TYR cc_start: 0.8906 (m-10) cc_final: 0.8643 (m-80) REVERT: B 362 ASP cc_start: 0.7986 (m-30) cc_final: 0.6570 (m-30) REVERT: B 379 SER cc_start: 0.9142 (t) cc_final: 0.8369 (t) REVERT: B 586 TYR cc_start: 0.9190 (m-80) cc_final: 0.8597 (m-80) REVERT: B 599 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: B 612 TYR cc_start: 0.8476 (m-80) cc_final: 0.7948 (m-80) REVERT: B 615 MET cc_start: 0.9262 (mmm) cc_final: 0.8601 (mmp) REVERT: B 628 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 667 LEU cc_start: 0.8470 (tt) cc_final: 0.8264 (tt) REVERT: B 668 ASN cc_start: 0.8440 (m-40) cc_final: 0.8142 (m110) REVERT: C 21 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8277 (t80) REVERT: C 24 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7798 (mm-40) REVERT: C 134 LYS cc_start: 0.9335 (pttt) cc_final: 0.8931 (tppt) REVERT: C 149 ASP cc_start: 0.8532 (t0) cc_final: 0.8274 (t0) REVERT: C 242 TYR cc_start: 0.9139 (t80) cc_final: 0.8806 (t80) REVERT: C 245 ASP cc_start: 0.9163 (t70) cc_final: 0.8809 (m-30) REVERT: C 270 ASN cc_start: 0.8808 (m-40) cc_final: 0.8560 (m-40) REVERT: C 276 TYR cc_start: 0.7986 (t80) cc_final: 0.7654 (t80) REVERT: C 318 ASP cc_start: 0.9011 (m-30) cc_final: 0.8772 (m-30) REVERT: D 96 MET cc_start: 0.7260 (mmt) cc_final: 0.7016 (mmt) REVERT: D 137 MET cc_start: 0.6131 (mtp) cc_final: 0.5750 (mmt) REVERT: D 154 PHE cc_start: 0.9270 (t80) cc_final: 0.8873 (t80) REVERT: D 169 TYR cc_start: 0.8700 (m-80) cc_final: 0.8274 (m-80) REVERT: D 183 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6343 (ptpp) REVERT: D 186 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8379 (mp10) REVERT: D 213 TYR cc_start: 0.9031 (t80) cc_final: 0.8720 (t80) REVERT: D 236 TYR cc_start: 0.7869 (t80) cc_final: 0.7595 (t80) REVERT: D 263 ASN cc_start: 0.8505 (p0) cc_final: 0.8066 (p0) outliers start: 54 outliers final: 33 residues processed: 579 average time/residue: 0.1297 time to fit residues: 112.8189 Evaluate side-chains 573 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 533 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 131 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 210 GLN ** D 238 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096956 restraints weight = 28828.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.100500 restraints weight = 11946.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.102642 restraints weight = 6896.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103831 restraints weight = 4898.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104575 restraints weight = 4016.421| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16299 Z= 0.178 Angle : 0.672 12.738 22004 Z= 0.350 Chirality : 0.045 0.318 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.760 62.343 2264 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.09 % Allowed : 26.60 % Favored : 70.30 % 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: 0.96 (0.19), residues: 1928 helix: 1.05 (0.15), residues: 1142 sheet: -0.40 (0.41), residues: 144 loop : 0.37 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.024 0.001 TYR C 262 PHE 0.048 0.002 PHE D 227 TRP 0.024 0.002 TRP C 124 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (16298) covalent geometry : angle 0.67163 / 0.35 (22004) hydrogen bonds : bond 0.03919 / 2.47 ( 896) hydrogen bonds : angle 5.13676 / 3.62 ( 2616) Misc. bond : bond 0.00058 / 0.03 ( 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 592 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 539 time to evaluate : 0.651 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 102 ASN cc_start: 0.8891 (m-40) cc_final: 0.8396 (t0) REVERT: A 228 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8709 (mmtt) REVERT: A 266 LYS cc_start: 0.8988 (mttt) cc_final: 0.8700 (mttt) REVERT: A 286 ASP cc_start: 0.8655 (m-30) cc_final: 0.7745 (m-30) REVERT: A 322 MET cc_start: 0.8068 (mmt) cc_final: 0.7801 (tpp) REVERT: A 344 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 345 LYS cc_start: 0.9118 (tptm) cc_final: 0.8869 (tttp) REVERT: A 355 TYR cc_start: 0.8927 (m-80) cc_final: 0.8443 (m-80) REVERT: A 362 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: A 485 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.7642 (mtm110) REVERT: A 586 TYR cc_start: 0.8992 (m-10) cc_final: 0.8584 (m-10) REVERT: A 604 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7939 (mmt90) REVERT: A 639 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: A 684 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: B 15 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8079 (mp0) REVERT: B 98 PHE cc_start: 0.9273 (t80) cc_final: 0.8547 (t80) REVERT: B 109 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8463 (m-40) REVERT: B 121 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8814 (tpt170) REVERT: B 250 TYR cc_start: 0.9380 (m-80) cc_final: 0.7485 (m-80) REVERT: B 263 ASP cc_start: 0.8648 (m-30) cc_final: 0.8300 (m-30) REVERT: B 286 ASP cc_start: 0.7989 (m-30) cc_final: 0.7375 (m-30) REVERT: B 317 MET cc_start: 0.8403 (mtp) cc_final: 0.7580 (mtp) REVERT: B 342 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9345 (tt) REVERT: B 355 TYR cc_start: 0.8641 (m-80) cc_final: 0.8424 (m-80) REVERT: B 357 TYR cc_start: 0.9038 (m-10) cc_final: 0.8682 (m-80) REVERT: B 362 ASP cc_start: 0.8003 (m-30) cc_final: 0.6541 (m-30) REVERT: B 379 SER cc_start: 0.9121 (t) cc_final: 0.8403 (t) REVERT: B 402 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 599 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: B 612 TYR cc_start: 0.8514 (m-80) cc_final: 0.7999 (m-80) REVERT: B 628 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 659 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8086 (mmmt) REVERT: B 668 ASN cc_start: 0.8624 (m-40) cc_final: 0.8273 (m110) REVERT: B 686 ARG cc_start: 0.7666 (mpt90) cc_final: 0.7441 (mmt-90) REVERT: C 21 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8378 (t80) REVERT: C 40 ASP cc_start: 0.8930 (p0) cc_final: 0.7826 (p0) REVERT: C 122 PHE cc_start: 0.8543 (m-80) cc_final: 0.8214 (m-80) REVERT: C 134 LYS cc_start: 0.9301 (pttt) cc_final: 0.8885 (tppt) REVERT: C 137 MET cc_start: 0.8308 (ptp) cc_final: 0.7951 (ptp) REVERT: C 149 ASP cc_start: 0.8539 (t0) cc_final: 0.8270 (t0) REVERT: C 242 TYR cc_start: 0.9122 (t80) cc_final: 0.8765 (t80) REVERT: C 245 ASP cc_start: 0.9157 (t70) cc_final: 0.8948 (m-30) REVERT: C 270 ASN cc_start: 0.8853 (m-40) cc_final: 0.8619 (m-40) REVERT: C 276 TYR cc_start: 0.8028 (t80) cc_final: 0.7730 (t80) REVERT: C 318 ASP cc_start: 0.9029 (m-30) cc_final: 0.8777 (m-30) REVERT: D 96 MET cc_start: 0.7284 (mmt) cc_final: 0.7073 (mmt) REVERT: D 137 MET cc_start: 0.6310 (mtp) cc_final: 0.5826 (mmt) REVERT: D 154 PHE cc_start: 0.9277 (t80) cc_final: 0.8879 (t80) REVERT: D 169 TYR cc_start: 0.8819 (m-80) cc_final: 0.8363 (m-80) REVERT: D 183 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6155 (ptpp) REVERT: D 186 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8392 (mp10) REVERT: D 213 TYR cc_start: 0.9065 (t80) cc_final: 0.8852 (t80) REVERT: D 263 ASN cc_start: 0.8441 (p0) cc_final: 0.8068 (p0) outliers start: 53 outliers final: 37 residues processed: 562 average time/residue: 0.1307 time to fit residues: 110.3920 Evaluate side-chains 563 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 517 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 180 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3745 r_free = 0.3745 target = 0.140994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099394 restraints weight = 28880.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102961 restraints weight = 11924.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105100 restraints weight = 6893.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106350 restraints weight = 4903.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107058 restraints weight = 3990.732| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.6245 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= 0.144 Angle : 0.683 12.620 22004 Z= 0.356 Chirality : 0.045 0.312 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.649 61.358 2264 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.63 % Allowed : 27.19 % Favored : 70.19 % 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: 0.88 (0.19), residues: 1928 helix: 1.00 (0.15), residues: 1149 sheet: -0.36 (0.42), residues: 144 loop : 0.29 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.032 0.001 TYR D 236 PHE 0.053 0.002 PHE D 227 TRP 0.027 0.002 TRP C 124 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16298) covalent geometry : angle 0.68331 / 0.36 (22004) hydrogen bonds : bond 0.03855 / 2.43 ( 896) hydrogen bonds : angle 5.12382 / 3.61 ( 2616) Misc. bond : bond 0.00061 / 0.03 ( 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 577 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 532 time to evaluate : 0.640 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 102 ASN cc_start: 0.8930 (m-40) cc_final: 0.8411 (t0) REVERT: A 228 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8707 (mmtt) REVERT: A 266 LYS cc_start: 0.8995 (mttt) cc_final: 0.8679 (mttt) REVERT: A 286 ASP cc_start: 0.8643 (m-30) cc_final: 0.7899 (m-30) REVERT: A 322 MET cc_start: 0.8005 (mmt) cc_final: 0.7736 (tpp) REVERT: A 344 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 345 LYS cc_start: 0.9043 (tptm) cc_final: 0.8721 (tttp) REVERT: A 355 TYR cc_start: 0.8853 (m-80) cc_final: 0.8423 (m-80) REVERT: A 362 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6681 (m-30) REVERT: A 485 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.7685 (mtm110) REVERT: A 586 TYR cc_start: 0.8987 (m-10) cc_final: 0.8764 (m-10) REVERT: A 639 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: A 684 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: B 15 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8043 (mp0) REVERT: B 98 PHE cc_start: 0.9241 (t80) cc_final: 0.8464 (t80) REVERT: B 109 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: B 121 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8784 (tpt170) REVERT: B 250 TYR cc_start: 0.9352 (m-80) cc_final: 0.7502 (m-80) REVERT: B 263 ASP cc_start: 0.8636 (m-30) cc_final: 0.8396 (m-30) REVERT: B 286 ASP cc_start: 0.8003 (m-30) cc_final: 0.7280 (m-30) REVERT: B 317 MET cc_start: 0.8394 (mtp) cc_final: 0.7617 (mtp) REVERT: B 355 TYR cc_start: 0.8575 (m-80) cc_final: 0.8363 (m-80) REVERT: B 357 TYR cc_start: 0.8923 (m-10) cc_final: 0.8649 (m-80) REVERT: B 362 ASP cc_start: 0.8010 (m-30) cc_final: 0.6640 (m-30) REVERT: B 379 SER cc_start: 0.9105 (t) cc_final: 0.8332 (t) REVERT: B 586 TYR cc_start: 0.9205 (m-80) cc_final: 0.8589 (m-80) REVERT: B 599 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: B 612 TYR cc_start: 0.8488 (m-80) cc_final: 0.7981 (m-80) REVERT: C 20 MET cc_start: 0.8235 (ptp) cc_final: 0.8003 (ptp) REVERT: C 21 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8473 (t80) REVERT: C 24 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7736 (mm-40) REVERT: C 91 ASN cc_start: 0.9224 (m-40) cc_final: 0.8936 (m-40) REVERT: C 105 TYR cc_start: 0.8247 (m-80) cc_final: 0.7893 (m-80) REVERT: C 149 ASP cc_start: 0.8605 (t0) cc_final: 0.8350 (t0) REVERT: C 183 LYS cc_start: 0.7956 (pttm) cc_final: 0.6646 (ptpt) REVERT: C 233 ASN cc_start: 0.8844 (m110) cc_final: 0.8386 (p0) REVERT: C 245 ASP cc_start: 0.9140 (t70) cc_final: 0.8936 (m-30) REVERT: C 261 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.7925 (mtm180) REVERT: C 270 ASN cc_start: 0.8814 (m-40) cc_final: 0.8583 (m-40) REVERT: C 276 TYR cc_start: 0.8074 (t80) cc_final: 0.7872 (t80) REVERT: C 318 ASP cc_start: 0.9019 (m-30) cc_final: 0.8779 (m-30) REVERT: D 46 TYR cc_start: 0.8898 (m-10) cc_final: 0.8550 (m-10) REVERT: D 96 MET cc_start: 0.7173 (mmt) cc_final: 0.6933 (mmt) REVERT: D 137 MET cc_start: 0.6496 (mtp) cc_final: 0.6009 (mmt) REVERT: D 154 PHE cc_start: 0.9282 (t80) cc_final: 0.8883 (t80) REVERT: D 169 TYR cc_start: 0.8813 (m-80) cc_final: 0.8343 (m-80) REVERT: D 183 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.6099 (ptpp) REVERT: D 213 TYR cc_start: 0.9073 (t80) cc_final: 0.8863 (t80) REVERT: D 263 ASN cc_start: 0.8378 (p0) cc_final: 0.8027 (p0) outliers start: 45 outliers final: 30 residues processed: 552 average time/residue: 0.1295 time to fit residues: 107.2616 Evaluate side-chains 552 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 514 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 191 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 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 = 0.3753 r_free = 0.3753 target = 0.140976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.099736 restraints weight = 28846.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103273 restraints weight = 11799.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105383 restraints weight = 6810.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106604 restraints weight = 4841.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107338 restraints weight = 3967.472| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16299 Z= 0.144 Angle : 0.708 18.519 22004 Z= 0.367 Chirality : 0.044 0.318 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.592 61.445 2264 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.45 % Allowed : 27.60 % Favored : 69.95 % 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: 0.81 (0.19), residues: 1928 helix: 0.95 (0.15), residues: 1158 sheet: -0.49 (0.42), residues: 148 loop : 0.26 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 225 TYR 0.038 0.001 TYR C 247 PHE 0.051 0.002 PHE D 227 TRP 0.029 0.002 TRP C 124 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (16298) covalent geometry : angle 0.70798 / 0.37 (22004) hydrogen bonds : bond 0.03845 / 2.42 ( 896) hydrogen bonds : angle 5.13101 / 3.60 ( 2616) Misc. bond : bond 0.00065 / 0.03 ( 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 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 526 time to evaluate : 0.587 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 228 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8703 (mmtt) REVERT: A 266 LYS cc_start: 0.9005 (mttt) cc_final: 0.8727 (mttt) REVERT: A 286 ASP cc_start: 0.8692 (m-30) cc_final: 0.8039 (m-30) REVERT: A 322 MET cc_start: 0.8040 (mmt) cc_final: 0.7772 (tpp) REVERT: A 344 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 345 LYS cc_start: 0.9046 (tptm) cc_final: 0.8759 (tttp) REVERT: A 355 TYR cc_start: 0.8849 (m-80) cc_final: 0.8416 (m-80) REVERT: A 362 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: A 485 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.7671 (mtm110) REVERT: A 493 MET cc_start: 0.9068 (tmm) cc_final: 0.8831 (tmm) REVERT: A 639 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: A 684 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: B 15 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8017 (mp0) REVERT: B 98 PHE cc_start: 0.9247 (t80) cc_final: 0.8423 (t80) REVERT: B 121 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8796 (tpt170) REVERT: B 211 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7869 (mm-30) REVERT: B 250 TYR cc_start: 0.9339 (m-80) cc_final: 0.7461 (m-80) REVERT: B 263 ASP cc_start: 0.8712 (m-30) cc_final: 0.8319 (m-30) REVERT: B 286 ASP cc_start: 0.8046 (m-30) cc_final: 0.7347 (m-30) REVERT: B 317 MET cc_start: 0.8395 (mtp) cc_final: 0.7622 (mtp) REVERT: B 355 TYR cc_start: 0.8520 (m-80) cc_final: 0.8316 (m-80) REVERT: B 357 TYR cc_start: 0.8916 (m-10) cc_final: 0.8620 (m-80) REVERT: B 362 ASP cc_start: 0.7980 (m-30) cc_final: 0.6602 (m-30) REVERT: B 379 SER cc_start: 0.9086 (t) cc_final: 0.8250 (t) REVERT: B 586 TYR cc_start: 0.9149 (m-80) cc_final: 0.8573 (m-80) REVERT: B 612 TYR cc_start: 0.8463 (m-80) cc_final: 0.7962 (m-80) REVERT: B 634 MET cc_start: 0.8598 (mmm) cc_final: 0.8392 (tpp) REVERT: C 20 MET cc_start: 0.8337 (ptp) cc_final: 0.8075 (ptp) REVERT: C 21 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8479 (t80) REVERT: C 24 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7742 (mm-40) REVERT: C 82 ASP cc_start: 0.8372 (m-30) cc_final: 0.7933 (p0) REVERT: C 91 ASN cc_start: 0.9218 (m-40) cc_final: 0.8931 (m-40) REVERT: C 105 TYR cc_start: 0.8300 (m-80) cc_final: 0.7929 (m-80) REVERT: C 134 LYS cc_start: 0.9167 (pttt) cc_final: 0.8757 (tppt) REVERT: C 137 MET cc_start: 0.8425 (ptp) cc_final: 0.8183 (ptt) REVERT: C 149 ASP cc_start: 0.8648 (t0) cc_final: 0.8395 (t0) REVERT: C 183 LYS cc_start: 0.7907 (pttm) cc_final: 0.6722 (ptpt) REVERT: C 233 ASN cc_start: 0.8872 (m110) cc_final: 0.8342 (p0) REVERT: C 270 ASN cc_start: 0.8833 (m-40) cc_final: 0.8602 (m-40) REVERT: C 318 ASP cc_start: 0.9018 (m-30) cc_final: 0.8797 (m-30) REVERT: D 30 TRP cc_start: 0.8483 (p-90) cc_final: 0.8261 (p-90) REVERT: D 46 TYR cc_start: 0.8904 (m-10) cc_final: 0.8601 (m-10) REVERT: D 96 MET cc_start: 0.7241 (mmt) cc_final: 0.7041 (mmt) REVERT: D 137 MET cc_start: 0.6499 (mtp) cc_final: 0.6020 (mmt) REVERT: D 169 TYR cc_start: 0.8808 (m-80) cc_final: 0.8299 (m-80) REVERT: D 183 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5969 (ptpp) REVERT: D 263 ASN cc_start: 0.8345 (p0) cc_final: 0.7969 (p0) outliers start: 42 outliers final: 31 residues processed: 543 average time/residue: 0.1274 time to fit residues: 104.4237 Evaluate side-chains 544 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 507 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN ** D 238 ASN ** 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 = 0.3744 r_free = 0.3744 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098753 restraints weight = 28930.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102281 restraints weight = 11967.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104329 restraints weight = 6906.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105557 restraints weight = 4965.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106239 restraints weight = 4052.598| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 16299 Z= 0.275 Angle : 0.899 59.193 22004 Z= 0.503 Chirality : 0.050 0.514 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.608 61.538 2264 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.50 % Favored : 98.44 % Rotamer: Outliers : 2.16 % Allowed : 28.00 % Favored : 69.84 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1928 helix: 0.91 (0.15), residues: 1158 sheet: -0.47 (0.42), residues: 148 loop : 0.26 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 604 TYR 0.059 0.002 TYR C 276 PHE 0.051 0.002 PHE D 227 TRP 0.025 0.003 TRP C 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.28 (16298) covalent geometry : angle 0.89918 / 0.50 (22004) hydrogen bonds : bond 0.03883 / 2.47 ( 896) hydrogen bonds : angle 5.15556 / 3.63 ( 2616) Misc. bond : bond 0.00064 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3464.24 seconds wall clock time: 60 minutes 48.73 seconds (3648.73 seconds total)