Starting phenix.real_space_refine on Thu Aug 6 14:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx8_44999/08_2026/9bx8_44999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx8_44999/08_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_44999/08_2026/9bx8_44999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx8_44999/08_2026/9bx8_44999.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx8_44999/08_2026/9bx8_44999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx8_44999/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2.85, per 1000 atoms: 0.18 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: 1.05 Conformation dependent library (CDL) restraints added in 607.7 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: 0.39 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: 2.83 Time building geometry restraints manager: 1.36 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 2.320 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 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 ... (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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.180 Find NCS groups from input model: 0.220 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- 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 : 0.428 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: 0.4489 (m-30) REVERT: C 92 PHE cc_start: 0.7840 (t80) cc_final: 0.7527 (t80) REVERT: C 131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6465 (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: 0.6593 (m-80) outliers start: 25 outliers final: 4 residues processed: 882 average time/residue: 0.1132 time to fit residues: 146.3639 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 : 0.412 ------------------------------------------------------------------------------- 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 192 ASN ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104906 restraints weight = 28152.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108900 restraints weight = 11906.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111297 restraints weight = 6898.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112681 restraints weight = 4867.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113674 restraints weight = 3942.840| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 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 = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (14 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16299 Z= 0.146 Angle : 0.642 10.696 22004 Z= 0.343 Chirality : 0.044 0.207 2348 Planarity : 0.004 0.057 2812 Dihedral : 7.035 62.437 2270 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.44 % Allowed : 17.79 % Favored : 78.76 % 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: 1.49 (0.18), residues: 1928 helix: 1.38 (0.15), residues: 1132 sheet: 1.43 (0.44), residues: 96 loop : 0.44 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.030 0.002 TYR C 173 PHE 0.032 0.002 PHE B 261 TRP 0.030 0.003 TRP C 124 HIS 0.020 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (16298) covalent geometry : angle 0.64179 / 0.34 (22004) hydrogen bonds : bond 0.04642 / 2.90 ( 896) hydrogen bonds : angle 5.17806 / 3.60 ( 2616) Misc. bond : bond 0.00246 / 0.13 ( 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: 59 poor density : 697 time to evaluate : 0.601 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 107 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: A 246 SER cc_start: 0.7313 (m) cc_final: 0.6760 (p) REVERT: A 286 ASP cc_start: 0.8712 (m-30) cc_final: 0.7527 (m-30) REVERT: A 312 GLN cc_start: 0.8665 (pt0) cc_final: 0.8317 (pt0) REVERT: A 344 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 362 ASP cc_start: 0.7524 (m-30) cc_final: 0.6756 (m-30) REVERT: A 379 SER cc_start: 0.9126 (t) cc_final: 0.8817 (t) REVERT: A 406 ASP cc_start: 0.8102 (m-30) cc_final: 0.7899 (m-30) REVERT: A 535 ASP cc_start: 0.8178 (t0) cc_final: 0.7784 (t0) REVERT: A 640 MET cc_start: 0.9069 (tpp) cc_final: 0.7852 (tpp) REVERT: A 668 ASN cc_start: 0.9232 (m-40) cc_final: 0.9021 (m110) REVERT: B 109 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8717 (m-40) REVERT: B 250 TYR cc_start: 0.9293 (m-80) cc_final: 0.8013 (m-80) REVERT: B 263 ASP cc_start: 0.8854 (m-30) cc_final: 0.8512 (m-30) REVERT: B 286 ASP cc_start: 0.8043 (m-30) cc_final: 0.7167 (m-30) REVERT: B 321 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 334 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8736 (ptpp) REVERT: B 355 TYR cc_start: 0.8741 (m-80) cc_final: 0.8441 (m-80) REVERT: B 357 TYR cc_start: 0.9021 (m-10) cc_final: 0.8587 (m-80) REVERT: B 362 ASP cc_start: 0.7833 (m-30) cc_final: 0.6680 (m-30) REVERT: B 379 SER cc_start: 0.9302 (t) cc_final: 0.8388 (t) REVERT: B 586 TYR cc_start: 0.8712 (m-80) cc_final: 0.8441 (m-80) REVERT: B 598 MET cc_start: 0.8256 (mtm) cc_final: 0.7646 (mtp) REVERT: B 599 GLU cc_start: 0.8266 (pm20) cc_final: 0.7804 (pm20) REVERT: B 604 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8103 (tpp80) REVERT: B 628 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7644 (mm-30) REVERT: C 21 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8238 (t80) REVERT: C 25 ASN cc_start: 0.8449 (m-40) cc_final: 0.7921 (m-40) REVERT: C 42 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7514 (pp) REVERT: C 92 PHE cc_start: 0.8369 (t80) cc_final: 0.7895 (t80) REVERT: C 95 MET cc_start: 0.8427 (tmm) cc_final: 0.8105 (tmm) REVERT: C 97 GLU cc_start: 0.5067 (mm-30) cc_final: 0.4213 (mm-30) REVERT: C 122 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8180 (m-10) REVERT: C 183 LYS cc_start: 0.8082 (pttt) cc_final: 0.7846 (pttp) REVERT: C 212 ILE cc_start: 0.9032 (mt) cc_final: 0.8816 (mp) REVERT: C 213 TYR cc_start: 0.7717 (t80) cc_final: 0.7480 (t80) REVERT: C 227 PHE cc_start: 0.8314 (t80) cc_final: 0.8021 (t80) REVERT: C 242 TYR cc_start: 0.8966 (t80) cc_final: 0.8519 (t80) REVERT: C 260 ILE cc_start: 0.8139 (pt) cc_final: 0.7856 (pt) REVERT: C 283 ASN cc_start: 0.7481 (p0) cc_final: 0.7185 (p0) REVERT: D 17 PHE cc_start: 0.5810 (m-80) cc_final: 0.5295 (m-80) REVERT: D 23 ASN cc_start: 0.9367 (m-40) cc_final: 0.9145 (t0) REVERT: D 27 LYS cc_start: 0.8993 (mttt) cc_final: 0.8718 (pttp) REVERT: D 42 LEU cc_start: 0.8802 (tp) cc_final: 0.8494 (mp) REVERT: D 117 THR cc_start: 0.8883 (m) cc_final: 0.7845 (m) REVERT: D 119 ASN cc_start: 0.7756 (m-40) cc_final: 0.7539 (m-40) REVERT: D 137 MET cc_start: 0.4494 (mtp) cc_final: 0.3929 (mmm) REVERT: D 154 PHE cc_start: 0.9287 (t80) cc_final: 0.8763 (t80) REVERT: D 157 MET cc_start: 0.9120 (mtp) cc_final: 0.8774 (ptp) REVERT: D 169 TYR cc_start: 0.8160 (m-80) cc_final: 0.7687 (m-80) REVERT: D 213 TYR cc_start: 0.8072 (t80) cc_final: 0.7650 (t80) REVERT: D 215 LYS cc_start: 0.8873 (mtmp) cc_final: 0.8653 (mtmm) REVERT: D 244 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7831 (pt0) outliers start: 59 outliers final: 17 residues processed: 718 average time/residue: 0.1034 time to fit residues: 112.3298 Evaluate side-chains 600 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 577 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 107 LYS 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 286 VAL 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: 0.8980 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 125 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 370 ASN A 387 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 475 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 263 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN D 233 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098475 restraints weight = 29047.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102047 restraints weight = 12211.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104185 restraints weight = 7108.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105554 restraints weight = 5018.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106307 restraints weight = 4043.166| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 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 (11 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16299 Z= 0.175 Angle : 0.611 8.899 22004 Z= 0.328 Chirality : 0.043 0.153 2348 Planarity : 0.004 0.054 2812 Dihedral : 6.904 61.464 2267 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.15 % Allowed : 20.36 % Favored : 76.49 % 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: 1.35 (0.15), residues: 1140 sheet: 0.66 (0.41), residues: 124 loop : 0.43 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.022 0.002 TYR C 236 PHE 0.034 0.002 PHE D 172 TRP 0.024 0.002 TRP D 30 HIS 0.025 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (16298) covalent geometry : angle 0.61055 / 0.33 (22004) hydrogen bonds : bond 0.04227 / 2.63 ( 896) hydrogen bonds : angle 5.04873 / 3.52 ( 2616) Misc. bond : bond 0.00122 / 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 667 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 613 time to evaluate : 0.508 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: A 246 SER cc_start: 0.7165 (m) cc_final: 0.6591 (p) REVERT: A 286 ASP cc_start: 0.8666 (m-30) cc_final: 0.7596 (m-30) REVERT: A 312 GLN cc_start: 0.8690 (pt0) cc_final: 0.8422 (pt0) REVERT: A 344 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 362 ASP cc_start: 0.7773 (m-30) cc_final: 0.6662 (m-30) REVERT: A 485 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8123 (mtm-85) REVERT: A 604 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7397 (ttm110) REVERT: B 98 PHE cc_start: 0.9266 (t80) cc_final: 0.8793 (t80) REVERT: B 250 TYR cc_start: 0.9366 (m-80) cc_final: 0.7921 (m-80) REVERT: B 286 ASP cc_start: 0.8039 (m-30) cc_final: 0.7311 (m-30) REVERT: B 318 ASP cc_start: 0.8366 (t0) cc_final: 0.7714 (t0) REVERT: B 355 TYR cc_start: 0.8781 (m-80) cc_final: 0.8439 (m-80) REVERT: B 357 TYR cc_start: 0.8995 (m-10) cc_final: 0.8653 (m-80) REVERT: B 362 ASP cc_start: 0.8097 (m-30) cc_final: 0.6925 (m-30) REVERT: B 379 SER cc_start: 0.9198 (t) cc_final: 0.8411 (t) REVERT: B 426 GLU cc_start: 0.8378 (pm20) cc_final: 0.8085 (pm20) REVERT: B 466 MET cc_start: 0.8664 (ptm) cc_final: 0.8249 (ptm) REVERT: B 493 MET cc_start: 0.9478 (tmm) cc_final: 0.9154 (tmm) REVERT: B 586 TYR cc_start: 0.9148 (m-80) cc_final: 0.8471 (m-80) REVERT: B 599 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: B 602 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 603 GLU cc_start: 0.8188 (tp30) cc_final: 0.7560 (tp30) REVERT: B 612 TYR cc_start: 0.8520 (m-80) cc_final: 0.6813 (m-80) REVERT: B 628 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 668 ASN cc_start: 0.8619 (m-40) cc_final: 0.8365 (m110) REVERT: C 20 MET cc_start: 0.8048 (tpt) cc_final: 0.7511 (ptp) REVERT: C 21 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8240 (t80) REVERT: C 25 ASN cc_start: 0.8765 (m-40) cc_final: 0.8307 (m-40) REVERT: C 37 LEU cc_start: 0.5989 (mp) cc_final: 0.5174 (mt) REVERT: C 42 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7773 (pp) REVERT: C 92 PHE cc_start: 0.8286 (t80) cc_final: 0.7788 (t80) REVERT: C 95 MET cc_start: 0.8477 (tmm) cc_final: 0.8023 (tmm) REVERT: C 97 GLU cc_start: 0.4386 (mm-30) cc_final: 0.4063 (mm-30) REVERT: C 105 TYR cc_start: 0.7498 (m-80) cc_final: 0.7191 (m-80) REVERT: C 122 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: C 145 ILE cc_start: 0.8622 (tp) cc_final: 0.8238 (tp) REVERT: C 178 PHE cc_start: 0.9204 (m-10) cc_final: 0.8798 (m-80) REVERT: C 227 PHE cc_start: 0.8568 (t80) cc_final: 0.8050 (t80) REVERT: C 231 LEU cc_start: 0.9310 (mm) cc_final: 0.8879 (pp) REVERT: C 242 TYR cc_start: 0.9009 (t80) cc_final: 0.8705 (t80) REVERT: D 23 ASN cc_start: 0.9357 (m-40) cc_final: 0.9128 (t0) REVERT: D 27 LYS cc_start: 0.8980 (mttt) cc_final: 0.8721 (pttp) REVERT: D 42 LEU cc_start: 0.8744 (tp) cc_final: 0.8254 (mp) REVERT: D 46 TYR cc_start: 0.8877 (m-10) cc_final: 0.8335 (m-10) REVERT: D 117 THR cc_start: 0.8380 (m) cc_final: 0.8133 (m) REVERT: D 137 MET cc_start: 0.5005 (mtp) cc_final: 0.4622 (mmt) REVERT: D 154 PHE cc_start: 0.9295 (t80) cc_final: 0.8740 (t80) REVERT: D 169 TYR cc_start: 0.8232 (m-80) cc_final: 0.7886 (m-80) REVERT: D 186 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8352 (mp10) REVERT: D 193 LEU cc_start: 0.9353 (mt) cc_final: 0.8974 (mp) REVERT: D 196 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7799 (ttp80) REVERT: D 213 TYR cc_start: 0.8346 (t80) cc_final: 0.7729 (t80) REVERT: D 242 TYR cc_start: 0.7860 (t80) cc_final: 0.7465 (t80) REVERT: D 244 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7994 (pt0) REVERT: D 315 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8951 (mp) outliers start: 54 outliers final: 36 residues processed: 636 average time/residue: 0.1068 time to fit residues: 102.7159 Evaluate side-chains 609 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 568 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 227 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 ILE 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 188 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 440 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 96 MET Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 211 GLU 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 287 LEU Chi-restraints excluded: chain D residue 315 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: 3.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 145 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN A 668 ASN B 44 ASN B 131 ASN B 304 HIS B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 263 ASN C 265 ASN D 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.096138 restraints weight = 28737.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099765 restraints weight = 11959.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102087 restraints weight = 6866.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103427 restraints weight = 4795.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104348 restraints weight = 3864.528| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16299 Z= 0.145 Angle : 0.611 14.356 22004 Z= 0.322 Chirality : 0.043 0.162 2348 Planarity : 0.004 0.053 2812 Dihedral : 6.718 61.075 2266 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.15 % Allowed : 21.41 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1928 helix: 1.39 (0.15), residues: 1131 sheet: 0.52 (0.42), residues: 124 loop : 0.38 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 164 TYR 0.021 0.001 TYR C 262 PHE 0.033 0.002 PHE D 172 TRP 0.025 0.002 TRP D 30 HIS 0.025 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16298) covalent geometry : angle 0.61106 / 0.32 (22004) hydrogen bonds : bond 0.03941 / 2.45 ( 896) hydrogen bonds : angle 4.99068 / 3.49 ( 2616) Misc. bond : bond 0.00098 / 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 637 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 583 time to evaluate : 0.514 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 228 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8616 (mmtt) REVERT: A 246 SER cc_start: 0.7060 (m) cc_final: 0.6554 (p) REVERT: A 266 LYS cc_start: 0.9011 (mttt) cc_final: 0.8788 (mttp) REVERT: A 286 ASP cc_start: 0.8734 (m-30) cc_final: 0.7800 (m-30) REVERT: A 316 GLU cc_start: 0.8641 (tp30) cc_final: 0.7991 (mp0) REVERT: A 344 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 362 ASP cc_start: 0.7866 (m-30) cc_final: 0.6804 (m-30) REVERT: A 485 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7698 (mtm180) REVERT: A 550 MET cc_start: 0.8556 (mtp) cc_final: 0.8232 (mtm) REVERT: A 604 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7547 (ttm110) REVERT: A 639 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: B 98 PHE cc_start: 0.9317 (t80) cc_final: 0.8796 (t80) REVERT: B 109 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8027 (m-40) REVERT: B 250 TYR cc_start: 0.9370 (m-80) cc_final: 0.7718 (m-80) REVERT: B 286 ASP cc_start: 0.8217 (m-30) cc_final: 0.7457 (m-30) REVERT: B 355 TYR cc_start: 0.8753 (m-80) cc_final: 0.8494 (m-80) REVERT: B 362 ASP cc_start: 0.8068 (m-30) cc_final: 0.6767 (m-30) REVERT: B 379 SER cc_start: 0.9172 (t) cc_final: 0.8293 (t) REVERT: B 493 MET cc_start: 0.9502 (tmm) cc_final: 0.9074 (tmm) REVERT: B 586 TYR cc_start: 0.9084 (m-80) cc_final: 0.8569 (m-80) REVERT: B 599 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: B 602 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 603 GLU cc_start: 0.8333 (tp30) cc_final: 0.7616 (tp30) REVERT: B 604 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8477 (tpp80) REVERT: B 612 TYR cc_start: 0.8719 (m-80) cc_final: 0.7589 (m-80) REVERT: B 628 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7871 (mm-30) REVERT: C 20 MET cc_start: 0.8077 (tpt) cc_final: 0.7660 (ptt) REVERT: C 21 PHE cc_start: 0.8886 (m-80) cc_final: 0.8255 (t80) REVERT: C 25 ASN cc_start: 0.8890 (m-40) cc_final: 0.8562 (m-40) REVERT: C 42 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7755 (pt) REVERT: C 74 MET cc_start: 0.7139 (mmm) cc_final: 0.6627 (mmm) REVERT: C 92 PHE cc_start: 0.8394 (t80) cc_final: 0.8102 (t80) REVERT: C 95 MET cc_start: 0.8510 (tmm) cc_final: 0.8198 (tmm) REVERT: C 105 TYR cc_start: 0.7818 (m-80) cc_final: 0.7444 (m-80) REVERT: C 122 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: C 227 PHE cc_start: 0.8654 (t80) cc_final: 0.8388 (t80) REVERT: C 242 TYR cc_start: 0.9243 (t80) cc_final: 0.8773 (t80) REVERT: C 321 TYR cc_start: 0.8454 (m-80) cc_final: 0.7859 (m-80) REVERT: D 17 PHE cc_start: 0.5354 (m-80) cc_final: 0.5047 (m-80) REVERT: D 27 LYS cc_start: 0.9010 (mttt) cc_final: 0.8738 (pttp) REVERT: D 42 LEU cc_start: 0.8669 (tp) cc_final: 0.8395 (mp) REVERT: D 56 MET cc_start: 0.7074 (mmm) cc_final: 0.6564 (ptp) REVERT: D 117 THR cc_start: 0.8387 (m) cc_final: 0.8111 (m) REVERT: D 137 MET cc_start: 0.5202 (mtp) cc_final: 0.4690 (mmt) REVERT: D 154 PHE cc_start: 0.9306 (t80) cc_final: 0.8637 (t80) REVERT: D 186 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8308 (mp10) REVERT: D 193 LEU cc_start: 0.9368 (mt) cc_final: 0.8888 (mp) REVERT: D 196 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7827 (ttp80) REVERT: D 213 TYR cc_start: 0.8462 (t80) cc_final: 0.7915 (t80) REVERT: D 233 ASN cc_start: 0.8167 (m-40) cc_final: 0.7957 (m110) REVERT: D 236 TYR cc_start: 0.7775 (t80) cc_final: 0.7266 (t80) REVERT: D 242 TYR cc_start: 0.8098 (t80) cc_final: 0.7777 (t80) REVERT: D 263 ASN cc_start: 0.8549 (p0) cc_final: 0.8116 (p0) outliers start: 54 outliers final: 25 residues processed: 605 average time/residue: 0.1029 time to fit residues: 93.8447 Evaluate side-chains 564 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 534 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 653 SER 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 342 LEU 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 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU 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 191 ILE Chi-restraints excluded: chain C residue 196 ARG 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 189 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 131 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 84 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093737 restraints weight = 29074.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097310 restraints weight = 12382.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.099514 restraints weight = 7224.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100781 restraints weight = 5136.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101409 restraints weight = 4170.827| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16299 Z= 0.234 Angle : 0.653 12.495 22004 Z= 0.347 Chirality : 0.045 0.177 2348 Planarity : 0.004 0.053 2812 Dihedral : 7.001 64.076 2264 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.08 % Allowed : 22.52 % Favored : 73.40 % 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: 1.24 (0.15), residues: 1132 sheet: -0.50 (0.39), residues: 152 loop : 0.43 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.023 0.002 TYR C 236 PHE 0.025 0.002 PHE C 178 TRP 0.024 0.003 TRP D 30 HIS 0.025 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (16298) covalent geometry : angle 0.65260 / 0.35 (22004) hydrogen bonds : bond 0.04034 / 2.56 ( 896) hydrogen bonds : angle 5.10842 / 3.59 ( 2616) Misc. bond : bond 0.00089 / 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 633 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 563 time to evaluate : 0.605 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 144 MET cc_start: 0.8605 (mtm) cc_final: 0.8175 (mtm) REVERT: A 228 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8697 (mmtt) REVERT: A 266 LYS cc_start: 0.9045 (mttt) cc_final: 0.8830 (mttp) REVERT: A 286 ASP cc_start: 0.8619 (m-30) cc_final: 0.7738 (m-30) REVERT: A 344 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 362 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.6702 (m-30) REVERT: A 384 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.6431 (pm20) REVERT: A 485 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8260 (mtm110) REVERT: A 586 TYR cc_start: 0.8986 (m-80) cc_final: 0.8625 (m-10) REVERT: A 602 GLU cc_start: 0.7963 (tt0) cc_final: 0.7281 (tt0) REVERT: A 604 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7722 (ttm110) REVERT: A 639 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: A 684 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 98 PHE cc_start: 0.9373 (t80) cc_final: 0.8719 (t80) REVERT: B 109 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8698 (m-40) REVERT: B 167 LEU cc_start: 0.9119 (mt) cc_final: 0.8621 (mp) REVERT: B 250 TYR cc_start: 0.9425 (m-80) cc_final: 0.7464 (m-80) REVERT: B 263 ASP cc_start: 0.8732 (m-30) cc_final: 0.8383 (m-30) REVERT: B 286 ASP cc_start: 0.8095 (m-30) cc_final: 0.7419 (m-30) REVERT: B 342 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9289 (tt) REVERT: B 355 TYR cc_start: 0.8802 (m-80) cc_final: 0.8519 (m-80) REVERT: B 362 ASP cc_start: 0.7989 (m-30) cc_final: 0.6546 (m-30) REVERT: B 379 SER cc_start: 0.9143 (t) cc_final: 0.8329 (t) REVERT: B 586 TYR cc_start: 0.9142 (m-80) cc_final: 0.8608 (m-80) REVERT: B 602 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7666 (tm-30) REVERT: B 612 TYR cc_start: 0.8677 (m-80) cc_final: 0.7947 (m-80) REVERT: B 624 PHE cc_start: 0.8780 (t80) cc_final: 0.8499 (t80) REVERT: B 625 PHE cc_start: 0.9184 (m-10) cc_final: 0.8875 (m-10) REVERT: B 628 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 659 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7568 (mmmt) REVERT: C 20 MET cc_start: 0.8169 (tpt) cc_final: 0.7588 (ptp) REVERT: C 21 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8305 (t80) REVERT: C 25 ASN cc_start: 0.9054 (m-40) cc_final: 0.8849 (m-40) REVERT: C 40 ASP cc_start: 0.8835 (p0) cc_final: 0.8561 (p0) REVERT: C 42 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7741 (pp) REVERT: C 74 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6741 (mmm) REVERT: C 82 ASP cc_start: 0.8513 (m-30) cc_final: 0.7835 (p0) REVERT: C 92 PHE cc_start: 0.8460 (t80) cc_final: 0.8155 (t80) REVERT: C 95 MET cc_start: 0.8673 (tmm) cc_final: 0.8252 (tmm) REVERT: C 122 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: C 178 PHE cc_start: 0.9229 (m-80) cc_final: 0.8741 (m-10) REVERT: C 183 LYS cc_start: 0.7858 (pttt) cc_final: 0.7524 (pttp) REVERT: C 192 ASN cc_start: 0.8953 (p0) cc_final: 0.8631 (p0) REVERT: C 193 LEU cc_start: 0.8698 (mt) cc_final: 0.8467 (mm) REVERT: C 227 PHE cc_start: 0.8753 (t80) cc_final: 0.8358 (t80) REVERT: C 231 LEU cc_start: 0.9370 (mm) cc_final: 0.8886 (pp) REVERT: C 242 TYR cc_start: 0.9199 (t80) cc_final: 0.8625 (t80) REVERT: C 270 ASN cc_start: 0.8782 (m-40) cc_final: 0.8554 (m-40) REVERT: C 276 TYR cc_start: 0.8175 (t80) cc_final: 0.7800 (t80) REVERT: D 17 PHE cc_start: 0.5688 (m-80) cc_final: 0.5254 (m-80) REVERT: D 46 TYR cc_start: 0.8914 (m-10) cc_final: 0.8664 (m-10) REVERT: D 56 MET cc_start: 0.7468 (mmm) cc_final: 0.6515 (ptp) REVERT: D 86 ARG cc_start: 0.7942 (mmt180) cc_final: 0.7659 (mpt-90) REVERT: D 137 MET cc_start: 0.6014 (mtp) cc_final: 0.5623 (mmt) REVERT: D 154 PHE cc_start: 0.9327 (t80) cc_final: 0.8845 (t80) REVERT: D 186 GLN cc_start: 0.8645 (mm110) cc_final: 0.8369 (mp10) REVERT: D 213 TYR cc_start: 0.9082 (t80) cc_final: 0.8800 (t80) REVERT: D 233 ASN cc_start: 0.8322 (m-40) cc_final: 0.8100 (m110) REVERT: D 236 TYR cc_start: 0.7835 (t80) cc_final: 0.7389 (t80) REVERT: D 242 TYR cc_start: 0.8315 (t80) cc_final: 0.7988 (t80) REVERT: D 263 ASN cc_start: 0.8606 (p0) cc_final: 0.8210 (p0) REVERT: D 315 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8879 (mt) outliers start: 70 outliers final: 39 residues processed: 590 average time/residue: 0.1017 time to fit residues: 90.6348 Evaluate side-chains 570 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 520 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP 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 495 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP 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 109 ASN Chi-restraints excluded: chain B residue 155 THR 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 441 GLU Chi-restraints excluded: chain B residue 584 ILE 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 74 MET Chi-restraints excluded: chain C residue 96 MET 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 252 LEU 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 200 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 0.0000 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 28 GLN D 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.099456 restraints weight = 28620.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103139 restraints weight = 11983.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105281 restraints weight = 6903.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106546 restraints weight = 4896.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107307 restraints weight = 3966.554| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 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 = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16299 Z= 0.135 Angle : 0.629 11.912 22004 Z= 0.330 Chirality : 0.043 0.166 2348 Planarity : 0.004 0.052 2812 Dihedral : 6.740 60.662 2264 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.21 % Allowed : 24.45 % Favored : 72.35 % 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: 1.09 (0.19), residues: 1928 helix: 1.18 (0.15), residues: 1146 sheet: -0.55 (0.40), residues: 152 loop : 0.43 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.023 0.001 TYR C 142 PHE 0.028 0.002 PHE D 172 TRP 0.025 0.002 TRP D 30 HIS 0.026 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16298) covalent geometry : angle 0.62949 / 0.33 (22004) hydrogen bonds : bond 0.03767 / 2.37 ( 896) hydrogen bonds : angle 5.00233 / 3.51 ( 2616) Misc. bond : bond 0.00084 / 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 630 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 575 time to evaluate : 0.398 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 29 ASP cc_start: 0.8878 (t0) cc_final: 0.8613 (t70) REVERT: A 102 ASN cc_start: 0.8847 (m-40) cc_final: 0.8465 (t0) REVERT: A 228 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8725 (mmtt) REVERT: A 286 ASP cc_start: 0.8639 (m-30) cc_final: 0.7796 (m-30) REVERT: A 344 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 355 TYR cc_start: 0.8877 (m-80) cc_final: 0.8469 (m-80) REVERT: A 362 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.6612 (m-30) REVERT: A 485 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: A 586 TYR cc_start: 0.8967 (m-80) cc_final: 0.8666 (m-10) REVERT: A 602 GLU cc_start: 0.7920 (tt0) cc_final: 0.7686 (tt0) REVERT: A 639 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: A 684 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: A 688 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7115 (pptt) REVERT: B 98 PHE cc_start: 0.9239 (t80) cc_final: 0.8574 (t80) REVERT: B 109 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: B 167 LEU cc_start: 0.9068 (mt) cc_final: 0.8580 (mp) REVERT: B 250 TYR cc_start: 0.9366 (m-80) cc_final: 0.7539 (m-80) REVERT: B 263 ASP cc_start: 0.8675 (m-30) cc_final: 0.8289 (m-30) REVERT: B 286 ASP cc_start: 0.8090 (m-30) cc_final: 0.7383 (m-30) REVERT: B 355 TYR cc_start: 0.8616 (m-80) cc_final: 0.8341 (m-80) REVERT: B 357 TYR cc_start: 0.8928 (m-10) cc_final: 0.8612 (m-80) REVERT: B 362 ASP cc_start: 0.7997 (m-30) cc_final: 0.6520 (m-30) REVERT: B 379 SER cc_start: 0.9135 (t) cc_final: 0.8272 (t) REVERT: B 586 TYR cc_start: 0.9124 (m-80) cc_final: 0.8641 (m-80) REVERT: B 602 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 603 GLU cc_start: 0.8364 (tp30) cc_final: 0.8129 (tp30) REVERT: B 612 TYR cc_start: 0.8496 (m-80) cc_final: 0.7935 (m-80) REVERT: B 615 MET cc_start: 0.9239 (mmm) cc_final: 0.8706 (mmp) REVERT: B 628 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7972 (mt-10) REVERT: B 671 ASP cc_start: 0.7752 (m-30) cc_final: 0.7542 (m-30) REVERT: C 20 MET cc_start: 0.8087 (tpt) cc_final: 0.7732 (ptp) REVERT: C 21 PHE cc_start: 0.8990 (m-80) cc_final: 0.8320 (t80) REVERT: C 40 ASP cc_start: 0.8730 (p0) cc_final: 0.8127 (p0) REVERT: C 74 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6766 (mmm) REVERT: C 82 ASP cc_start: 0.8513 (m-30) cc_final: 0.7878 (p0) REVERT: C 92 PHE cc_start: 0.8433 (t80) cc_final: 0.8144 (t80) REVERT: C 95 MET cc_start: 0.8680 (tmm) cc_final: 0.8414 (tmm) REVERT: C 105 TYR cc_start: 0.7913 (m-80) cc_final: 0.7521 (m-80) REVERT: C 107 ASN cc_start: 0.8862 (p0) cc_final: 0.8343 (p0) REVERT: C 122 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: C 183 LYS cc_start: 0.7905 (pttt) cc_final: 0.7698 (pttp) REVERT: C 192 ASN cc_start: 0.8902 (p0) cc_final: 0.8499 (p0) REVERT: C 227 PHE cc_start: 0.8696 (t80) cc_final: 0.8350 (t80) REVERT: C 231 LEU cc_start: 0.9360 (mm) cc_final: 0.8930 (pp) REVERT: C 233 ASN cc_start: 0.8724 (m110) cc_final: 0.8283 (p0) REVERT: C 242 TYR cc_start: 0.9184 (t80) cc_final: 0.8668 (t80) REVERT: C 270 ASN cc_start: 0.8770 (m-40) cc_final: 0.8526 (m-40) REVERT: C 276 TYR cc_start: 0.8031 (t80) cc_final: 0.7722 (t80) REVERT: D 46 TYR cc_start: 0.8916 (m-10) cc_final: 0.8607 (m-10) REVERT: D 86 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7615 (mpt-90) REVERT: D 131 LEU cc_start: 0.7887 (tp) cc_final: 0.7687 (tt) REVERT: D 137 MET cc_start: 0.6127 (mtp) cc_final: 0.5702 (mmt) REVERT: D 154 PHE cc_start: 0.9332 (t80) cc_final: 0.8918 (t80) REVERT: D 169 TYR cc_start: 0.8575 (m-80) cc_final: 0.8115 (m-80) REVERT: D 186 GLN cc_start: 0.8636 (mm110) cc_final: 0.8399 (mp10) REVERT: D 207 LEU cc_start: 0.9466 (mm) cc_final: 0.9235 (mm) REVERT: D 213 TYR cc_start: 0.9103 (t80) cc_final: 0.8594 (t80) REVERT: D 236 TYR cc_start: 0.7797 (t80) cc_final: 0.7518 (t80) REVERT: D 263 ASN cc_start: 0.8536 (p0) cc_final: 0.8061 (p0) REVERT: D 315 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8811 (mt) outliers start: 55 outliers final: 34 residues processed: 596 average time/residue: 0.1037 time to fit residues: 93.3300 Evaluate side-chains 572 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 530 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 218 ASN Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR 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 421 GLU 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 74 MET 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 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 200 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN B 474 GLN C 25 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 = 0.3764 r_free = 0.3764 target = 0.142007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099841 restraints weight = 28504.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103492 restraints weight = 11781.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105642 restraints weight = 6815.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106908 restraints weight = 4866.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107624 restraints weight = 3981.648| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16299 Z= 0.135 Angle : 0.648 12.379 22004 Z= 0.337 Chirality : 0.043 0.217 2348 Planarity : 0.003 0.051 2812 Dihedral : 6.637 60.866 2264 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.86 % Allowed : 25.55 % Favored : 71.59 % 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: 1.07 (0.19), residues: 1928 helix: 1.16 (0.15), residues: 1145 sheet: -0.32 (0.41), residues: 142 loop : 0.34 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 669 TYR 0.019 0.001 TYR D 22 PHE 0.026 0.001 PHE C 172 TRP 0.031 0.002 TRP D 30 HIS 0.029 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (16298) covalent geometry : angle 0.64842 / 0.34 (22004) hydrogen bonds : bond 0.03782 / 2.39 ( 896) hydrogen bonds : angle 5.01124 / 3.52 ( 2616) Misc. bond : bond 0.00069 / 0.04 ( 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 601 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 552 time to evaluate : 0.618 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 29 ASP cc_start: 0.8862 (t0) cc_final: 0.8597 (t70) REVERT: A 102 ASN cc_start: 0.8848 (m-40) cc_final: 0.8460 (t0) REVERT: A 228 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8749 (mmtt) REVERT: A 266 LYS cc_start: 0.8807 (mttt) cc_final: 0.8538 (mttp) REVERT: A 286 ASP cc_start: 0.8661 (m-30) cc_final: 0.7890 (m-30) REVERT: A 344 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 355 TYR cc_start: 0.8861 (m-80) cc_final: 0.8511 (m-80) REVERT: A 362 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: A 406 ASP cc_start: 0.8173 (m-30) cc_final: 0.7864 (m-30) REVERT: A 485 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.7649 (mtm110) REVERT: A 586 TYR cc_start: 0.8955 (m-80) cc_final: 0.8455 (m-10) REVERT: A 602 GLU cc_start: 0.7852 (tt0) cc_final: 0.6586 (tt0) REVERT: A 639 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: A 683 TYR cc_start: 0.8922 (t80) cc_final: 0.8552 (t80) REVERT: A 684 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: A 688 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7099 (pptt) REVERT: B 15 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8128 (mp0) REVERT: B 98 PHE cc_start: 0.9250 (t80) cc_final: 0.8543 (t80) REVERT: B 109 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8468 (m-40) REVERT: B 121 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8767 (tpt170) REVERT: B 167 LEU cc_start: 0.9068 (mt) cc_final: 0.8559 (mp) REVERT: B 250 TYR cc_start: 0.9350 (m-80) cc_final: 0.7512 (m-80) REVERT: B 263 ASP cc_start: 0.8662 (m-30) cc_final: 0.8285 (m-30) REVERT: B 286 ASP cc_start: 0.8055 (m-30) cc_final: 0.7295 (m-30) REVERT: B 317 MET cc_start: 0.8598 (mtp) cc_final: 0.7846 (mtp) REVERT: B 355 TYR cc_start: 0.8553 (m-80) cc_final: 0.8339 (m-80) REVERT: B 357 TYR cc_start: 0.8935 (m-10) cc_final: 0.8660 (m-80) REVERT: B 362 ASP cc_start: 0.7946 (m-30) cc_final: 0.6529 (m-30) REVERT: B 379 SER cc_start: 0.9162 (t) cc_final: 0.8349 (t) REVERT: B 586 TYR cc_start: 0.9103 (m-80) cc_final: 0.8590 (m-80) REVERT: B 603 GLU cc_start: 0.8301 (tp30) cc_final: 0.8030 (tp30) REVERT: B 612 TYR cc_start: 0.8489 (m-80) cc_final: 0.7930 (m-80) REVERT: B 615 MET cc_start: 0.9218 (mmm) cc_final: 0.8573 (mmp) REVERT: B 628 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 668 ASN cc_start: 0.8650 (m110) cc_final: 0.8334 (m110) REVERT: C 20 MET cc_start: 0.8074 (tpt) cc_final: 0.7755 (ptp) REVERT: C 21 PHE cc_start: 0.8981 (m-80) cc_final: 0.8287 (t80) REVERT: C 30 TRP cc_start: 0.7808 (p-90) cc_final: 0.7147 (p-90) REVERT: C 40 ASP cc_start: 0.8813 (p0) cc_final: 0.8096 (p0) REVERT: C 82 ASP cc_start: 0.8518 (m-30) cc_final: 0.7900 (p0) REVERT: C 92 PHE cc_start: 0.8493 (t80) cc_final: 0.8203 (t80) REVERT: C 95 MET cc_start: 0.8705 (tmm) cc_final: 0.8361 (tmm) REVERT: C 105 TYR cc_start: 0.8029 (m-80) cc_final: 0.7565 (m-80) REVERT: C 107 ASN cc_start: 0.8916 (p0) cc_final: 0.8709 (p0) REVERT: C 122 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7996 (m-10) REVERT: C 134 LYS cc_start: 0.9325 (pttt) cc_final: 0.8944 (tppt) REVERT: C 227 PHE cc_start: 0.8724 (t80) cc_final: 0.8388 (t80) REVERT: C 231 LEU cc_start: 0.9391 (mm) cc_final: 0.8958 (pp) REVERT: C 233 ASN cc_start: 0.8820 (m110) cc_final: 0.8328 (p0) REVERT: C 270 ASN cc_start: 0.8816 (m-40) cc_final: 0.8553 (m-40) REVERT: C 276 TYR cc_start: 0.7915 (t80) cc_final: 0.7696 (t80) REVERT: D 46 TYR cc_start: 0.8905 (m-10) cc_final: 0.8596 (m-10) REVERT: D 86 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7657 (mpt-90) REVERT: D 137 MET cc_start: 0.6098 (mtp) cc_final: 0.5715 (mmt) REVERT: D 154 PHE cc_start: 0.9355 (t80) cc_final: 0.8918 (t80) REVERT: D 169 TYR cc_start: 0.8629 (m-80) cc_final: 0.8198 (m-80) REVERT: D 178 PHE cc_start: 0.9348 (m-80) cc_final: 0.8746 (m-80) REVERT: D 186 GLN cc_start: 0.8613 (mm110) cc_final: 0.8382 (mp10) REVERT: D 236 TYR cc_start: 0.7790 (t80) cc_final: 0.7463 (t80) REVERT: D 263 ASN cc_start: 0.8359 (p0) cc_final: 0.7924 (p0) REVERT: D 315 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8728 (mt) outliers start: 49 outliers final: 33 residues processed: 570 average time/residue: 0.1222 time to fit residues: 105.3088 Evaluate side-chains 570 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 529 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 240 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 589 SER 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 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 121 ARG 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 468 LEU Chi-restraints excluded: chain B residue 584 ILE 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 196 ARG 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 200 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 122 optimal weight: 0.0770 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 24 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.138215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095874 restraints weight = 28770.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099408 restraints weight = 12357.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101572 restraints weight = 7171.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102810 restraints weight = 5118.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103547 restraints weight = 4199.305| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16299 Z= 0.179 Angle : 0.675 12.002 22004 Z= 0.351 Chirality : 0.045 0.201 2348 Planarity : 0.004 0.051 2812 Dihedral : 6.767 63.087 2264 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.33 % Allowed : 25.96 % Favored : 70.71 % 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: 1.01 (0.19), residues: 1928 helix: 1.11 (0.15), residues: 1138 sheet: -0.43 (0.42), residues: 144 loop : 0.36 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 225 TYR 0.025 0.002 TYR C 262 PHE 0.027 0.002 PHE C 172 TRP 0.033 0.002 TRP D 30 HIS 0.031 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (16298) covalent geometry : angle 0.67495 / 0.35 (22004) hydrogen bonds : bond 0.03842 / 2.43 ( 896) hydrogen bonds : angle 5.07800 / 3.58 ( 2616) Misc. bond : bond 0.00054 / 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 596 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 539 time to evaluate : 0.488 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 217 GLU cc_start: 0.8771 (mp0) cc_final: 0.8556 (mp0) REVERT: A 228 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8742 (mmtt) REVERT: A 266 LYS cc_start: 0.8823 (mttt) cc_final: 0.8526 (mttp) REVERT: A 286 ASP cc_start: 0.8646 (m-30) cc_final: 0.7765 (m-30) REVERT: A 344 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 355 TYR cc_start: 0.8893 (m-80) cc_final: 0.8454 (m-80) REVERT: A 362 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: A 485 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7647 (mtm110) REVERT: A 586 TYR cc_start: 0.8967 (m-80) cc_final: 0.8685 (m-10) REVERT: A 598 MET cc_start: 0.8440 (mtt) cc_final: 0.8144 (mtp) REVERT: A 639 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: A 684 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: B 15 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8102 (mp0) REVERT: B 98 PHE cc_start: 0.9317 (t80) cc_final: 0.8604 (t80) REVERT: B 109 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8456 (m-40) REVERT: B 167 LEU cc_start: 0.9120 (mt) cc_final: 0.8598 (mp) REVERT: B 250 TYR cc_start: 0.9401 (m-80) cc_final: 0.7419 (m-80) REVERT: B 263 ASP cc_start: 0.8668 (m-30) cc_final: 0.8290 (m-30) REVERT: B 286 ASP cc_start: 0.8072 (m-30) cc_final: 0.7462 (m-30) REVERT: B 317 MET cc_start: 0.8624 (mtp) cc_final: 0.7756 (mtp) REVERT: B 342 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9349 (tt) REVERT: B 357 TYR cc_start: 0.9093 (m-10) cc_final: 0.8737 (m-80) REVERT: B 362 ASP cc_start: 0.7979 (m-30) cc_final: 0.6524 (m-30) REVERT: B 379 SER cc_start: 0.9096 (t) cc_final: 0.8306 (t) REVERT: B 602 GLU cc_start: 0.7764 (tm-30) cc_final: 0.6697 (tm-30) REVERT: B 603 GLU cc_start: 0.8310 (tp30) cc_final: 0.7966 (tp30) REVERT: B 610 LYS cc_start: 0.8691 (tppt) cc_final: 0.8419 (tppt) REVERT: B 612 TYR cc_start: 0.8482 (m-80) cc_final: 0.7834 (m-80) REVERT: B 628 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 21 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8307 (t80) REVERT: C 40 ASP cc_start: 0.8847 (p0) cc_final: 0.8108 (p0) REVERT: C 49 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8266 (ttpp) REVERT: C 82 ASP cc_start: 0.8490 (m-30) cc_final: 0.7937 (p0) REVERT: C 92 PHE cc_start: 0.8282 (t80) cc_final: 0.7962 (t80) REVERT: C 95 MET cc_start: 0.8774 (tmm) cc_final: 0.8341 (tmm) REVERT: C 105 TYR cc_start: 0.8090 (m-80) cc_final: 0.7628 (m-80) REVERT: C 122 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: C 192 ASN cc_start: 0.8910 (p0) cc_final: 0.8474 (p0) REVERT: C 193 LEU cc_start: 0.8472 (mt) cc_final: 0.8180 (mp) REVERT: C 204 TYR cc_start: 0.8032 (t80) cc_final: 0.7591 (t80) REVERT: C 227 PHE cc_start: 0.8791 (t80) cc_final: 0.8473 (t80) REVERT: C 231 LEU cc_start: 0.9429 (mm) cc_final: 0.9023 (pp) REVERT: C 233 ASN cc_start: 0.8807 (m110) cc_final: 0.8308 (p0) REVERT: C 270 ASN cc_start: 0.8870 (m-40) cc_final: 0.8630 (m-40) REVERT: C 276 TYR cc_start: 0.7959 (t80) cc_final: 0.7733 (t80) REVERT: D 27 LYS cc_start: 0.8710 (pttt) cc_final: 0.8507 (pttp) REVERT: D 46 TYR cc_start: 0.8946 (m-10) cc_final: 0.8630 (m-10) REVERT: D 86 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7601 (mpt-90) REVERT: D 137 MET cc_start: 0.6367 (mtp) cc_final: 0.5890 (mmp) REVERT: D 154 PHE cc_start: 0.9337 (t80) cc_final: 0.8939 (t80) REVERT: D 169 TYR cc_start: 0.8772 (m-80) cc_final: 0.8304 (m-80) REVERT: D 177 TYR cc_start: 0.8687 (t80) cc_final: 0.8414 (t80) REVERT: D 186 GLN cc_start: 0.8586 (mm110) cc_final: 0.8336 (mp10) REVERT: D 236 TYR cc_start: 0.7713 (t80) cc_final: 0.7417 (t80) REVERT: D 263 ASN cc_start: 0.8426 (p0) cc_final: 0.8077 (p0) outliers start: 57 outliers final: 41 residues processed: 560 average time/residue: 0.1178 time to fit residues: 99.2527 Evaluate side-chains 570 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 522 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 240 MET Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET 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 589 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR 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 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 658 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR 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 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 196 ARG 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 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 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... B 25 GLN B 131 ASN C 24 GLN D 71 ASN D 181 GLN D 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098404 restraints weight = 28544.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101994 restraints weight = 11937.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104174 restraints weight = 6959.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105389 restraints weight = 4967.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106107 restraints weight = 4079.794| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6193 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= 0.141 Angle : 0.683 12.526 22004 Z= 0.354 Chirality : 0.044 0.214 2348 Planarity : 0.004 0.050 2812 Dihedral : 6.623 61.781 2264 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.68 % Allowed : 27.13 % 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: 0.91 (0.19), residues: 1928 helix: 1.02 (0.15), residues: 1154 sheet: 0.03 (0.44), residues: 130 loop : 0.17 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 225 TYR 0.036 0.001 TYR C 247 PHE 0.032 0.002 PHE C 178 TRP 0.029 0.002 TRP C 44 HIS 0.029 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16298) covalent geometry : angle 0.68342 / 0.35 (22004) hydrogen bonds : bond 0.03764 / 2.39 ( 896) hydrogen bonds : angle 5.03503 / 3.55 ( 2616) Misc. bond : bond 0.00067 / 0.04 ( 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 583 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 537 time to evaluate : 0.442 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 99 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8837 (mmtp) REVERT: A 102 ASN cc_start: 0.8873 (m-40) cc_final: 0.8357 (t0) REVERT: A 228 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8737 (mmtt) REVERT: A 286 ASP cc_start: 0.8655 (m-30) cc_final: 0.7940 (m-30) REVERT: A 344 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 355 TYR cc_start: 0.8862 (m-80) cc_final: 0.8515 (m-80) REVERT: A 362 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: A 485 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.7646 (mtm110) REVERT: A 639 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: A 683 TYR cc_start: 0.8889 (t80) cc_final: 0.8448 (t80) REVERT: A 684 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: B 15 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8017 (mp0) REVERT: B 98 PHE cc_start: 0.9311 (t80) cc_final: 0.8555 (t80) REVERT: B 109 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8486 (m-40) REVERT: B 167 LEU cc_start: 0.9100 (mt) cc_final: 0.8572 (mp) REVERT: B 250 TYR cc_start: 0.9350 (m-80) cc_final: 0.7365 (m-80) REVERT: B 263 ASP cc_start: 0.8698 (m-30) cc_final: 0.8319 (m-30) REVERT: B 286 ASP cc_start: 0.8087 (m-30) cc_final: 0.7488 (m-30) REVERT: B 357 TYR cc_start: 0.8972 (m-10) cc_final: 0.8661 (m-80) REVERT: B 362 ASP cc_start: 0.7962 (m-30) cc_final: 0.6601 (m-30) REVERT: B 379 SER cc_start: 0.9106 (t) cc_final: 0.8237 (t) REVERT: B 610 LYS cc_start: 0.8719 (tppt) cc_final: 0.8313 (tppt) REVERT: B 612 TYR cc_start: 0.8369 (m-80) cc_final: 0.7707 (m-80) REVERT: B 628 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8083 (mm-30) REVERT: B 659 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7921 (mmmt) REVERT: B 686 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7529 (mmt-90) REVERT: C 20 MET cc_start: 0.8097 (tpt) cc_final: 0.7862 (ptt) REVERT: C 21 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8320 (t80) REVERT: C 40 ASP cc_start: 0.8864 (p0) cc_final: 0.8109 (p0) REVERT: C 82 ASP cc_start: 0.8536 (m-30) cc_final: 0.7978 (p0) REVERT: C 92 PHE cc_start: 0.8148 (t80) cc_final: 0.7864 (t80) REVERT: C 95 MET cc_start: 0.8731 (tmm) cc_final: 0.8348 (tmm) REVERT: C 105 TYR cc_start: 0.8096 (m-80) cc_final: 0.7672 (m-80) REVERT: C 122 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: C 227 PHE cc_start: 0.8787 (t80) cc_final: 0.8489 (t80) REVERT: C 231 LEU cc_start: 0.9435 (mm) cc_final: 0.9033 (pp) REVERT: C 233 ASN cc_start: 0.8846 (m110) cc_final: 0.8418 (p0) REVERT: C 270 ASN cc_start: 0.8854 (m-40) cc_final: 0.8573 (m110) REVERT: D 46 TYR cc_start: 0.8954 (m-10) cc_final: 0.8636 (m-10) REVERT: D 137 MET cc_start: 0.6550 (mtp) cc_final: 0.6065 (mmt) REVERT: D 154 PHE cc_start: 0.9381 (t80) cc_final: 0.8977 (t80) REVERT: D 169 TYR cc_start: 0.8755 (m-80) cc_final: 0.8255 (m-80) REVERT: D 177 TYR cc_start: 0.8738 (t80) cc_final: 0.8426 (t80) REVERT: D 186 GLN cc_start: 0.8531 (mm110) cc_final: 0.8307 (mp10) REVERT: D 213 TYR cc_start: 0.9018 (t80) cc_final: 0.8765 (t80) REVERT: D 236 TYR cc_start: 0.7767 (t80) cc_final: 0.7442 (t80) REVERT: D 263 ASN cc_start: 0.8424 (p0) cc_final: 0.8052 (p0) outliers start: 46 outliers final: 32 residues processed: 553 average time/residue: 0.1032 time to fit residues: 86.2478 Evaluate side-chains 556 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 518 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 240 MET Chi-restraints excluded: chain A residue 348 MET 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 589 SER Chi-restraints excluded: chain A residue 604 ARG 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 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 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 196 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 57 optimal weight: 0.0770 chunk 121 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100668 restraints weight = 28650.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104320 restraints weight = 11900.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106513 restraints weight = 6883.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107795 restraints weight = 4906.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108489 restraints weight = 3994.277| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16299 Z= 0.143 Angle : 0.711 19.864 22004 Z= 0.364 Chirality : 0.044 0.231 2348 Planarity : 0.004 0.050 2812 Dihedral : 6.559 62.055 2264 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.33 % Allowed : 27.71 % 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: 0.89 (0.19), residues: 1928 helix: 1.03 (0.15), residues: 1154 sheet: -0.00 (0.44), residues: 130 loop : 0.13 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 225 TYR 0.029 0.001 TYR C 262 PHE 0.025 0.001 PHE C 172 TRP 0.028 0.002 TRP D 30 HIS 0.029 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (16298) covalent geometry : angle 0.71068 / 0.36 (22004) hydrogen bonds : bond 0.03774 / 2.38 ( 896) hydrogen bonds : angle 5.05770 / 3.57 ( 2616) Misc. bond : bond 0.00067 / 0.04 ( 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 562 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 522 time to evaluate : 0.610 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 99 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8796 (mmtp) REVERT: A 102 ASN cc_start: 0.8886 (m-40) cc_final: 0.8333 (t0) REVERT: A 228 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8758 (mmtt) REVERT: A 250 TYR cc_start: 0.8935 (m-80) cc_final: 0.7631 (m-80) REVERT: A 286 ASP cc_start: 0.8726 (m-30) cc_final: 0.8270 (m-30) REVERT: A 344 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 355 TYR cc_start: 0.8835 (m-80) cc_final: 0.8487 (m-80) REVERT: A 362 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: A 485 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8136 (mtm180) REVERT: A 493 MET cc_start: 0.9084 (tmm) cc_final: 0.8826 (tmm) REVERT: A 639 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: A 683 TYR cc_start: 0.8878 (t80) cc_final: 0.8520 (t80) REVERT: A 684 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: B 98 PHE cc_start: 0.9288 (t80) cc_final: 0.8533 (t80) REVERT: B 109 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8489 (m-40) REVERT: B 167 LEU cc_start: 0.9092 (mt) cc_final: 0.8558 (mp) REVERT: B 250 TYR cc_start: 0.9350 (m-80) cc_final: 0.7364 (m-80) REVERT: B 263 ASP cc_start: 0.8706 (m-30) cc_final: 0.8330 (m-30) REVERT: B 286 ASP cc_start: 0.8165 (m-30) cc_final: 0.7386 (m-30) REVERT: B 357 TYR cc_start: 0.8961 (m-10) cc_final: 0.8645 (m-80) REVERT: B 362 ASP cc_start: 0.7988 (m-30) cc_final: 0.6606 (m-30) REVERT: B 374 SER cc_start: 0.9324 (t) cc_final: 0.9041 (m) REVERT: B 379 SER cc_start: 0.9108 (t) cc_final: 0.8248 (t) REVERT: B 586 TYR cc_start: 0.9166 (m-80) cc_final: 0.8579 (m-80) REVERT: B 602 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 610 LYS cc_start: 0.8717 (tppt) cc_final: 0.8232 (tptp) REVERT: B 612 TYR cc_start: 0.8369 (m-80) cc_final: 0.7773 (m-80) REVERT: B 686 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7550 (mmt-90) REVERT: C 20 MET cc_start: 0.8030 (tpt) cc_final: 0.7791 (ptt) REVERT: C 21 PHE cc_start: 0.9066 (m-80) cc_final: 0.8370 (t80) REVERT: C 82 ASP cc_start: 0.8447 (m-30) cc_final: 0.7914 (p0) REVERT: C 91 ASN cc_start: 0.9210 (m-40) cc_final: 0.8976 (m-40) REVERT: C 105 TYR cc_start: 0.8184 (m-80) cc_final: 0.7745 (m-80) REVERT: C 122 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: C 134 LYS cc_start: 0.9122 (pttt) cc_final: 0.8778 (tppt) REVERT: C 137 MET cc_start: 0.8397 (ptp) cc_final: 0.8134 (ptp) REVERT: C 178 PHE cc_start: 0.9055 (m-10) cc_final: 0.8825 (m-10) REVERT: C 183 LYS cc_start: 0.7722 (pttm) cc_final: 0.6404 (ptpt) REVERT: C 227 PHE cc_start: 0.8786 (t80) cc_final: 0.8506 (t80) REVERT: C 231 LEU cc_start: 0.9435 (mm) cc_final: 0.9057 (pp) REVERT: C 233 ASN cc_start: 0.8915 (m110) cc_final: 0.8421 (p0) REVERT: C 270 ASN cc_start: 0.8860 (m-40) cc_final: 0.8657 (m-40) REVERT: D 28 GLN cc_start: 0.8830 (tt0) cc_final: 0.8627 (tm-30) REVERT: D 46 TYR cc_start: 0.8932 (m-10) cc_final: 0.8669 (m-10) REVERT: D 137 MET cc_start: 0.6583 (mtp) cc_final: 0.6050 (mmt) REVERT: D 169 TYR cc_start: 0.8774 (m-80) cc_final: 0.8275 (m-80) REVERT: D 177 TYR cc_start: 0.8659 (t80) cc_final: 0.8311 (t80) REVERT: D 186 GLN cc_start: 0.8555 (mm110) cc_final: 0.8352 (mp10) REVERT: D 236 TYR cc_start: 0.7736 (t80) cc_final: 0.7450 (t80) REVERT: D 263 ASN cc_start: 0.8418 (p0) cc_final: 0.8027 (p0) REVERT: D 315 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8729 (mt) outliers start: 40 outliers final: 32 residues processed: 536 average time/residue: 0.1051 time to fit residues: 85.9168 Evaluate side-chains 551 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 513 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 348 MET 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 589 SER Chi-restraints excluded: chain A residue 604 ARG 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 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 468 LEU Chi-restraints excluded: chain B residue 584 ILE 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 196 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 0.0670 chunk 146 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN B 320 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102008 restraints weight = 28617.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105614 restraints weight = 12000.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107822 restraints weight = 6853.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108991 restraints weight = 4829.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109797 restraints weight = 3957.071| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 16299 Z= 0.215 Angle : 0.909 59.198 22004 Z= 0.501 Chirality : 0.046 0.549 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.586 62.049 2264 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.50 % Favored : 98.44 % Rotamer: Outliers : 2.92 % Allowed : 27.48 % Favored : 69.60 % 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: 0.88 (0.19), residues: 1928 helix: 1.01 (0.15), residues: 1154 sheet: -0.00 (0.44), residues: 130 loop : 0.13 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 225 TYR 0.034 0.002 TYR C 276 PHE 0.026 0.002 PHE C 277 TRP 0.026 0.002 TRP D 30 HIS 0.029 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (16298) covalent geometry : angle 0.90884 / 0.50 (22004) hydrogen bonds : bond 0.03844 / 2.46 ( 896) hydrogen bonds : angle 5.07771 / 3.59 ( 2616) Misc. bond : bond 0.00062 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.99 seconds wall clock time: 51 minutes 24.33 seconds (3084.33 seconds total)