Starting phenix.real_space_refine on Thu Aug 6 14:52:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx3_44992/08_2026/9bx3_44992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx3_44992/08_2026/9bx3_44992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2026/9bx3_44992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2026/9bx3_44992.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2026/9bx3_44992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2026/9bx3_44992_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-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: 3.46, per 1000 atoms: 0.22 Number of scatterers: 15954 At special positions: 0 Unit cell: (91.98, 126.728, 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: 1.35 Conformation dependent library (CDL) restraints added in 588.3 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: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.553A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.705A 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: 3.792A 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: 3.521A 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: 4.273A 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: 3.950A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.961A 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: 3.778A 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: 4.621A 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: 4.175A 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: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A 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: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A 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: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.737A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A 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: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.78 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: 4974 1.34 - 1.46: 2945 1.46 - 1.58: 8204 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.607 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.30e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+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 1.11e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 21467 2.11 - 4.23: 464 4.23 - 6.34: 58 6.34 - 8.45: 8 8.45 - 10.57: 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 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.66 10.57 3.00e+00 1.11e-01 1.24e+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 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 8642 17.65 - 35.29: 855 35.29 - 52.94: 255 52.94 - 70.59: 64 70.59 - 88.24: 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 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+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 -134.35 11.75 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2122 0.093 - 0.187: 187 0.187 - 0.280: 33 0.280 - 0.374: 4 0.374 - 0.467: 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 5.46e+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 4.63e+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 5.53e-02 4.89e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+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 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.004 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: 131 2.51 - 3.11: 11873 3.11 - 3.70: 26426 3.70 - 4.30: 41198 4.30 - 4.90: 64928 Nonbonded interactions: 144556 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 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 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 1.965 2.320 ... (remaining 144551 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 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 0.834 16299 Z= 0.732 Angle : 0.756 10.566 22004 Z= 0.461 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.910 88.236 6168 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % 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: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 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 0.00585 / 0.33 (16298) covalent geometry : angle 0.75600 / 0.46 (22004) hydrogen bonds : bond 0.16171 / 10.53 ( 896) hydrogen bonds : angle 6.35194 / 4.48 ( 2616) Misc. bond : bond 0.83355 / 43.87 ( 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 883 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7477 (p0) cc_final: 0.7151 (p0) REVERT: A 35 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 200 SER cc_start: 0.8921 (t) cc_final: 0.8679 (t) REVERT: A 204 SER cc_start: 0.8532 (m) cc_final: 0.8297 (p) REVERT: A 349 LEU cc_start: 0.8108 (tp) cc_final: 0.7850 (tp) REVERT: A 359 MET cc_start: 0.7680 (ttt) cc_final: 0.7411 (ttt) REVERT: A 411 LEU cc_start: 0.8571 (mt) cc_final: 0.8292 (mt) REVERT: A 658 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 27 ASP cc_start: 0.7317 (p0) cc_final: 0.7082 (p0) REVERT: B 72 TYR cc_start: 0.7028 (m-80) cc_final: 0.6372 (m-10) REVERT: B 100 PHE cc_start: 0.8143 (t80) cc_final: 0.7863 (t80) REVERT: B 187 ASP cc_start: 0.7691 (t70) cc_final: 0.7430 (t0) REVERT: B 200 SER cc_start: 0.8916 (t) cc_final: 0.8319 (t) REVERT: B 211 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 235 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7601 (ttm-80) REVERT: B 246 SER cc_start: 0.8358 (m) cc_final: 0.7988 (p) REVERT: B 250 TYR cc_start: 0.8608 (m-80) cc_final: 0.8175 (m-80) REVERT: B 288 PHE cc_start: 0.8346 (t80) cc_final: 0.7903 (t80) REVERT: B 373 ILE cc_start: 0.8752 (mt) cc_final: 0.8165 (mt) REVERT: B 379 SER cc_start: 0.8708 (t) cc_final: 0.8091 (t) REVERT: B 415 ASN cc_start: 0.7985 (t0) cc_final: 0.7739 (t0) REVERT: B 420 MET cc_start: 0.8428 (mmm) cc_final: 0.8163 (mmm) REVERT: B 425 ILE cc_start: 0.9006 (mt) cc_final: 0.8711 (mt) REVERT: B 490 THR cc_start: 0.8636 (m) cc_final: 0.8411 (m) REVERT: B 494 MET cc_start: 0.7414 (mtp) cc_final: 0.7107 (mtp) REVERT: B 550 MET cc_start: 0.7872 (ttm) cc_final: 0.7311 (ttm) REVERT: B 558 TRP cc_start: 0.8481 (m100) cc_final: 0.8031 (m100) REVERT: B 626 TYR cc_start: 0.8053 (m-80) cc_final: 0.7768 (m-80) REVERT: C 157 MET cc_start: 0.7101 (mtt) cc_final: 0.6738 (mtp) REVERT: C 224 LEU cc_start: 0.4867 (mt) cc_final: 0.4572 (mt) REVERT: C 260 ILE cc_start: 0.6261 (pt) cc_final: 0.5525 (pt) REVERT: D 47 LEU cc_start: 0.4053 (mt) cc_final: 0.3757 (mp) REVERT: D 56 MET cc_start: 0.5125 (mmp) cc_final: 0.4713 (mtt) REVERT: D 67 THR cc_start: 0.7180 (m) cc_final: 0.6843 (m) REVERT: D 321 TYR cc_start: 0.6611 (m-80) cc_final: 0.6092 (t80) outliers start: 23 outliers final: 4 residues processed: 875 average time/residue: 0.1232 time to fit residues: 157.8325 Evaluate side-chains 606 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 600 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 14 ASN B 158 ASN B 645 GLN C 23 ASN C 25 ASN C 28 GLN C 52 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095934 restraints weight = 33710.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099538 restraints weight = 16588.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101818 restraints weight = 10073.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103243 restraints weight = 7102.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104141 restraints weight = 5586.008| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16299 Z= 0.194 Angle : 0.676 10.779 22004 Z= 0.361 Chirality : 0.044 0.180 2348 Planarity : 0.004 0.054 2812 Dihedral : 7.116 59.470 2273 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.33 % Allowed : 19.31 % Favored : 77.36 % 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: 1.47 (0.18), residues: 1928 helix: 1.36 (0.15), residues: 1124 sheet: 1.25 (0.43), residues: 98 loop : 0.49 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.030 0.002 TYR C 142 PHE 0.037 0.002 PHE C 168 TRP 0.023 0.002 TRP C 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16298) covalent geometry : angle 0.67606 / 0.36 (22004) hydrogen bonds : bond 0.04843 / 3.08 ( 896) hydrogen bonds : angle 5.30645 / 3.69 ( 2616) Misc. bond : bond 0.00134 / 0.07 ( 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 706 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 649 time to evaluate : 0.694 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: A 172 LEU cc_start: 0.9222 (mp) cc_final: 0.8429 (mp) REVERT: A 179 LEU cc_start: 0.9385 (tp) cc_final: 0.9127 (tp) REVERT: A 204 SER cc_start: 0.9030 (m) cc_final: 0.8828 (p) REVERT: A 218 ASN cc_start: 0.8457 (t0) cc_final: 0.8175 (t0) REVERT: A 315 ASP cc_start: 0.8026 (p0) cc_final: 0.7730 (p0) REVERT: A 316 GLU cc_start: 0.8144 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 355 TYR cc_start: 0.8241 (m-80) cc_final: 0.7979 (m-10) REVERT: A 383 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8426 (t) REVERT: A 406 ASP cc_start: 0.7988 (m-30) cc_final: 0.7318 (t0) REVERT: A 485 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7691 (mtt90) REVERT: A 493 MET cc_start: 0.8907 (tmm) cc_final: 0.8605 (tmm) REVERT: A 526 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 550 MET cc_start: 0.7727 (mtp) cc_final: 0.7309 (mtm) REVERT: A 646 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: A 662 MET cc_start: 0.8387 (mmp) cc_final: 0.8047 (mmp) REVERT: B 27 ASP cc_start: 0.8723 (p0) cc_final: 0.8450 (p0) REVERT: B 31 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: B 109 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8720 (m110) REVERT: B 161 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7595 (mtt180) REVERT: B 200 SER cc_start: 0.8946 (t) cc_final: 0.8239 (t) REVERT: B 232 ASN cc_start: 0.8964 (t0) cc_final: 0.8536 (m-40) REVERT: B 246 SER cc_start: 0.7701 (m) cc_final: 0.7318 (p) REVERT: B 250 TYR cc_start: 0.9265 (m-80) cc_final: 0.8063 (m-80) REVERT: B 288 PHE cc_start: 0.9298 (t80) cc_final: 0.9002 (t80) REVERT: B 379 SER cc_start: 0.8834 (t) cc_final: 0.8025 (t) REVERT: B 381 LEU cc_start: 0.9268 (tp) cc_final: 0.9067 (tp) REVERT: B 467 ASN cc_start: 0.9159 (t0) cc_final: 0.8544 (m-40) REVERT: B 480 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 586 TYR cc_start: 0.8428 (m-80) cc_final: 0.7957 (m-80) REVERT: B 590 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8164 (t) REVERT: B 591 THR cc_start: 0.9130 (p) cc_final: 0.8828 (p) REVERT: B 599 GLU cc_start: 0.8130 (pt0) cc_final: 0.7883 (pt0) REVERT: B 601 ILE cc_start: 0.9156 (mm) cc_final: 0.8383 (mm) REVERT: B 602 GLU cc_start: 0.8158 (tt0) cc_final: 0.7450 (tt0) REVERT: B 604 ARG cc_start: 0.8955 (mmp80) cc_final: 0.8236 (tpp-160) REVERT: B 628 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: B 640 MET cc_start: 0.9101 (tpp) cc_final: 0.8613 (tpp) REVERT: B 667 LEU cc_start: 0.9034 (tt) cc_final: 0.8459 (tt) REVERT: C 117 THR cc_start: 0.7871 (p) cc_final: 0.7660 (t) REVERT: C 178 PHE cc_start: 0.8305 (m-80) cc_final: 0.7678 (m-10) REVERT: C 193 LEU cc_start: 0.8637 (mm) cc_final: 0.8153 (mt) REVERT: C 224 LEU cc_start: 0.7522 (mt) cc_final: 0.7203 (mt) REVERT: C 239 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8420 (pp20) REVERT: D 56 MET cc_start: 0.3054 (mmp) cc_final: 0.2693 (mtt) REVERT: D 116 GLU cc_start: 0.8438 (pm20) cc_final: 0.8144 (pm20) REVERT: D 131 LEU cc_start: 0.8229 (tt) cc_final: 0.7375 (tt) REVERT: D 174 TYR cc_start: 0.4250 (t80) cc_final: 0.3639 (t80) REVERT: D 189 GLU cc_start: 0.8557 (tp30) cc_final: 0.7976 (mt-10) REVERT: D 204 TYR cc_start: 0.8829 (t80) cc_final: 0.8349 (t80) REVERT: D 216 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7689 (mp10) REVERT: D 224 LEU cc_start: 0.8960 (mt) cc_final: 0.8712 (mt) REVERT: D 277 PHE cc_start: 0.6243 (m-10) cc_final: 0.5927 (m-10) outliers start: 57 outliers final: 24 residues processed: 672 average time/residue: 0.1244 time to fit residues: 123.9281 Evaluate side-chains 593 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 563 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 44 ASN A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 43 GLN B 232 ASN B 370 ASN B 588 GLN ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 28 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.089556 restraints weight = 34719.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092796 restraints weight = 17042.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094835 restraints weight = 10382.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096262 restraints weight = 7345.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097140 restraints weight = 5723.367| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (17 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16299 Z= 0.294 Angle : 0.689 9.511 22004 Z= 0.371 Chirality : 0.045 0.161 2348 Planarity : 0.004 0.057 2812 Dihedral : 7.276 52.062 2267 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.43 % Allowed : 21.47 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 1928 helix: 1.21 (0.15), residues: 1142 sheet: -0.25 (0.39), residues: 152 loop : 0.52 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 196 TYR 0.028 0.002 TYR C 22 PHE 0.042 0.003 PHE C 168 TRP 0.016 0.002 TRP A 623 HIS 0.012 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.29 (16298) covalent geometry : angle 0.68933 / 0.37 (22004) hydrogen bonds : bond 0.04607 / 2.91 ( 896) hydrogen bonds : angle 5.32060 / 3.71 ( 2616) Misc. bond : bond 0.00029 / 0.02 ( 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 646 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 570 time to evaluate : 0.724 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: A 166 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 172 LEU cc_start: 0.9314 (mp) cc_final: 0.9026 (mp) REVERT: A 218 ASN cc_start: 0.8754 (t0) cc_final: 0.8524 (t0) REVERT: A 312 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: A 317 MET cc_start: 0.9152 (mtm) cc_final: 0.8454 (mtt) REVERT: A 322 MET cc_start: 0.8379 (tpp) cc_final: 0.7803 (tpp) REVERT: A 355 TYR cc_start: 0.8305 (m-80) cc_final: 0.8032 (m-10) REVERT: A 383 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8603 (t) REVERT: A 485 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.7635 (mtt90) REVERT: A 492 PHE cc_start: 0.9167 (m-10) cc_final: 0.8951 (m-10) REVERT: A 493 MET cc_start: 0.8854 (tmm) cc_final: 0.8421 (tmm) REVERT: A 608 ASN cc_start: 0.6634 (OUTLIER) cc_final: 0.6388 (t0) REVERT: B 31 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: B 161 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7804 (mtt180) REVERT: B 200 SER cc_start: 0.8963 (t) cc_final: 0.8276 (t) REVERT: B 228 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8281 (tppt) REVERT: B 232 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8625 (m-40) REVERT: B 246 SER cc_start: 0.7925 (m) cc_final: 0.7299 (p) REVERT: B 250 TYR cc_start: 0.9276 (m-80) cc_final: 0.8178 (m-80) REVERT: B 348 MET cc_start: 0.7604 (tpp) cc_final: 0.7384 (tpp) REVERT: B 379 SER cc_start: 0.8794 (t) cc_final: 0.8095 (t) REVERT: B 394 TYR cc_start: 0.9162 (m-80) cc_final: 0.8857 (m-80) REVERT: B 550 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7635 (ttm) REVERT: B 552 ILE cc_start: 0.9455 (mp) cc_final: 0.9219 (mt) REVERT: B 601 ILE cc_start: 0.9202 (mm) cc_final: 0.8150 (mm) REVERT: B 604 ARG cc_start: 0.8903 (mmp80) cc_final: 0.8299 (mmp80) REVERT: B 640 MET cc_start: 0.9043 (tpp) cc_final: 0.8628 (tpp) REVERT: B 670 ILE cc_start: 0.9282 (mm) cc_final: 0.9070 (mt) REVERT: C 56 MET cc_start: -0.4458 (tpt) cc_final: -0.4769 (tpp) REVERT: C 168 PHE cc_start: 0.7923 (m-80) cc_final: 0.7705 (m-80) REVERT: C 172 PHE cc_start: 0.7890 (m-10) cc_final: 0.7600 (m-10) REVERT: C 178 PHE cc_start: 0.8312 (m-80) cc_final: 0.7673 (m-10) REVERT: C 179 TYR cc_start: 0.8538 (t80) cc_final: 0.8171 (t80) REVERT: C 218 GLU cc_start: 0.9346 (mp0) cc_final: 0.8784 (pp20) REVERT: D 20 MET cc_start: 0.8672 (ppp) cc_final: 0.8468 (ppp) REVERT: D 103 LYS cc_start: 0.5889 (mptt) cc_final: 0.5606 (tppt) REVERT: D 131 LEU cc_start: 0.8248 (tt) cc_final: 0.7969 (mt) REVERT: D 174 TYR cc_start: 0.4127 (t80) cc_final: 0.3462 (t80) REVERT: D 179 TYR cc_start: 0.8104 (t80) cc_final: 0.7802 (t80) REVERT: D 204 TYR cc_start: 0.8847 (t80) cc_final: 0.8421 (t80) REVERT: D 216 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7615 (mm110) REVERT: D 242 TYR cc_start: 0.7686 (t80) cc_final: 0.7350 (t80) outliers start: 76 outliers final: 40 residues processed: 610 average time/residue: 0.1285 time to fit residues: 117.2171 Evaluate side-chains 546 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 500 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR 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: 0.9980 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 568 HIS A 646 GLN A 668 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093605 restraints weight = 34049.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097156 restraints weight = 16793.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099365 restraints weight = 10119.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100752 restraints weight = 7111.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101776 restraints weight = 5571.108| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16299 Z= 0.147 Angle : 0.627 9.128 22004 Z= 0.332 Chirality : 0.043 0.251 2348 Planarity : 0.004 0.053 2812 Dihedral : 7.022 57.550 2265 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.80 % Allowed : 23.92 % Favored : 73.28 % 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: 1.14 (0.19), residues: 1928 helix: 1.23 (0.15), residues: 1144 sheet: -0.11 (0.39), residues: 138 loop : 0.30 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.024 0.001 TYR D 236 PHE 0.032 0.002 PHE D 172 TRP 0.025 0.002 TRP C 30 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16298) covalent geometry : angle 0.62669 / 0.33 (22004) hydrogen bonds : bond 0.04170 / 2.64 ( 896) hydrogen bonds : angle 5.11637 / 3.55 ( 2616) Misc. bond : bond 0.00004 / 0.00 ( 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 632 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 584 time to evaluate : 0.593 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 218 ASN cc_start: 0.8745 (t0) cc_final: 0.8478 (t0) REVERT: A 322 MET cc_start: 0.8382 (tpp) cc_final: 0.8072 (tpp) REVERT: A 350 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7927 (mtp180) REVERT: A 355 TYR cc_start: 0.8219 (m-80) cc_final: 0.7996 (m-10) REVERT: A 366 LYS cc_start: 0.9470 (mtpt) cc_final: 0.9245 (ptpp) REVERT: A 383 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8731 (t) REVERT: A 485 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7625 (mtt90) REVERT: A 493 MET cc_start: 0.8889 (tmm) cc_final: 0.8618 (tmm) REVERT: A 612 TYR cc_start: 0.8907 (m-80) cc_final: 0.8536 (m-80) REVERT: A 640 MET cc_start: 0.8916 (tpp) cc_final: 0.8596 (tpp) REVERT: A 684 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 31 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: B 89 PHE cc_start: 0.8898 (t80) cc_final: 0.8656 (t80) REVERT: B 116 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8068 (mp0) REVERT: B 200 SER cc_start: 0.8870 (t) cc_final: 0.7944 (t) REVERT: B 228 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8325 (tppt) REVERT: B 232 ASN cc_start: 0.9060 (m-40) cc_final: 0.8683 (m-40) REVERT: B 246 SER cc_start: 0.7578 (m) cc_final: 0.7257 (p) REVERT: B 250 TYR cc_start: 0.9203 (m-80) cc_final: 0.8002 (m-80) REVERT: B 276 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8734 (mmtm) REVERT: B 348 MET cc_start: 0.7562 (tpp) cc_final: 0.7280 (tpp) REVERT: B 379 SER cc_start: 0.8668 (t) cc_final: 0.7464 (t) REVERT: B 494 MET cc_start: 0.8904 (mtp) cc_final: 0.8574 (mtp) REVERT: B 515 ASP cc_start: 0.8956 (m-30) cc_final: 0.8723 (m-30) REVERT: B 601 ILE cc_start: 0.9051 (mm) cc_final: 0.8677 (mm) REVERT: B 639 ASP cc_start: 0.8549 (m-30) cc_final: 0.7764 (m-30) REVERT: B 640 MET cc_start: 0.9059 (tpp) cc_final: 0.8683 (tpp) REVERT: B 670 ILE cc_start: 0.9274 (mm) cc_final: 0.9053 (mt) REVERT: B 677 ARG cc_start: 0.8971 (mmm160) cc_final: 0.8724 (mmm-85) REVERT: B 686 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7815 (mtm-85) REVERT: C 56 MET cc_start: -0.4890 (tpt) cc_final: -0.5137 (tpp) REVERT: C 168 PHE cc_start: 0.7998 (m-80) cc_final: 0.7774 (m-80) REVERT: C 172 PHE cc_start: 0.7754 (m-10) cc_final: 0.7531 (m-10) REVERT: C 178 PHE cc_start: 0.8345 (m-80) cc_final: 0.7823 (m-10) REVERT: C 179 TYR cc_start: 0.8487 (t80) cc_final: 0.8158 (t80) REVERT: D 18 THR cc_start: 0.6410 (p) cc_final: 0.6119 (p) REVERT: D 46 TYR cc_start: 0.8729 (m-10) cc_final: 0.8243 (m-80) REVERT: D 56 MET cc_start: 0.2296 (mmm) cc_final: 0.1950 (mpp) REVERT: D 120 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8734 (pp20) REVERT: D 131 LEU cc_start: 0.8324 (tt) cc_final: 0.7924 (mt) REVERT: D 174 TYR cc_start: 0.4123 (t80) cc_final: 0.3628 (t80) REVERT: D 176 LEU cc_start: 0.9366 (mt) cc_final: 0.9133 (tp) REVERT: D 204 TYR cc_start: 0.8762 (t80) cc_final: 0.8372 (t80) REVERT: D 242 TYR cc_start: 0.7753 (t80) cc_final: 0.7392 (t80) REVERT: D 281 ASP cc_start: 0.8367 (p0) cc_final: 0.7651 (t0) outliers start: 48 outliers final: 32 residues processed: 607 average time/residue: 0.1339 time to fit residues: 121.4166 Evaluate side-chains 562 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 527 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 588 GLN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092969 restraints weight = 34443.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096361 restraints weight = 17143.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098518 restraints weight = 10444.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099885 restraints weight = 7302.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100946 restraints weight = 5685.016| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16299 Z= 0.167 Angle : 0.649 12.461 22004 Z= 0.338 Chirality : 0.043 0.181 2348 Planarity : 0.004 0.051 2812 Dihedral : 7.059 59.778 2265 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.21 % Allowed : 24.68 % Favored : 72.11 % 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: 1.21 (0.15), residues: 1141 sheet: -0.31 (0.39), residues: 134 loop : 0.29 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.023 0.001 TYR B 613 PHE 0.028 0.002 PHE B 487 TRP 0.024 0.002 TRP C 30 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16298) covalent geometry : angle 0.64929 / 0.34 (22004) hydrogen bonds : bond 0.04059 / 2.54 ( 896) hydrogen bonds : angle 5.08687 / 3.53 ( 2616) Misc. bond : bond 0.00005 / 0.00 ( 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 617 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 562 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 218 ASN cc_start: 0.8793 (t0) cc_final: 0.8505 (t0) REVERT: A 312 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: A 322 MET cc_start: 0.8396 (tpp) cc_final: 0.7700 (tpp) REVERT: A 350 ARG cc_start: 0.8346 (mtp180) cc_final: 0.7937 (mtp180) REVERT: A 379 SER cc_start: 0.9305 (t) cc_final: 0.8997 (t) REVERT: A 383 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 406 ASP cc_start: 0.8106 (m-30) cc_final: 0.7732 (m-30) REVERT: A 485 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7642 (mtt90) REVERT: A 493 MET cc_start: 0.8941 (tmm) cc_final: 0.8441 (tmm) REVERT: A 599 GLU cc_start: 0.8429 (mp0) cc_final: 0.7759 (mp0) REVERT: A 640 MET cc_start: 0.8992 (tpp) cc_final: 0.8694 (tpp) REVERT: A 646 GLN cc_start: 0.9119 (mt0) cc_final: 0.8178 (mp10) REVERT: A 681 THR cc_start: 0.9032 (p) cc_final: 0.8714 (p) REVERT: A 684 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: B 65 GLU cc_start: 0.8352 (mp0) cc_final: 0.7454 (mp0) REVERT: B 89 PHE cc_start: 0.8980 (t80) cc_final: 0.8760 (t80) REVERT: B 116 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7920 (mp0) REVERT: B 200 SER cc_start: 0.8903 (t) cc_final: 0.8063 (t) REVERT: B 232 ASN cc_start: 0.9088 (t0) cc_final: 0.8595 (m-40) REVERT: B 246 SER cc_start: 0.7565 (m) cc_final: 0.7228 (p) REVERT: B 250 TYR cc_start: 0.9196 (m-80) cc_final: 0.8100 (m-80) REVERT: B 276 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8745 (mmtt) REVERT: B 348 MET cc_start: 0.7518 (tpp) cc_final: 0.7224 (tpp) REVERT: B 379 SER cc_start: 0.8866 (t) cc_final: 0.7553 (t) REVERT: B 394 TYR cc_start: 0.9099 (m-80) cc_final: 0.8812 (m-80) REVERT: B 494 MET cc_start: 0.8894 (mtp) cc_final: 0.8678 (mtp) REVERT: B 515 ASP cc_start: 0.8984 (m-30) cc_final: 0.8742 (m-30) REVERT: B 639 ASP cc_start: 0.8581 (m-30) cc_final: 0.7741 (m-30) REVERT: B 640 MET cc_start: 0.9075 (tpp) cc_final: 0.8741 (tpp) REVERT: B 670 ILE cc_start: 0.9265 (mm) cc_final: 0.9036 (mt) REVERT: B 677 ARG cc_start: 0.8954 (mmm160) cc_final: 0.8743 (mmm-85) REVERT: B 686 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7822 (mtm-85) REVERT: C 56 MET cc_start: -0.4765 (tpt) cc_final: -0.5073 (tpp) REVERT: C 168 PHE cc_start: 0.8106 (m-80) cc_final: 0.7871 (m-80) REVERT: C 172 PHE cc_start: 0.7824 (m-10) cc_final: 0.7419 (m-10) REVERT: C 178 PHE cc_start: 0.8374 (m-80) cc_final: 0.7848 (m-10) REVERT: C 179 TYR cc_start: 0.8464 (t80) cc_final: 0.8135 (t80) REVERT: C 181 GLN cc_start: 0.8177 (mm110) cc_final: 0.7853 (mm-40) REVERT: D 18 THR cc_start: 0.6366 (p) cc_final: 0.6041 (p) REVERT: D 46 TYR cc_start: 0.8776 (m-10) cc_final: 0.8310 (m-80) REVERT: D 120 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8704 (pp20) REVERT: D 174 TYR cc_start: 0.4359 (t80) cc_final: 0.3969 (t80) REVERT: D 176 LEU cc_start: 0.9397 (mt) cc_final: 0.9166 (tp) REVERT: D 204 TYR cc_start: 0.8800 (t80) cc_final: 0.8468 (t80) REVERT: D 211 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8565 (pt0) REVERT: D 281 ASP cc_start: 0.8529 (p0) cc_final: 0.8174 (t70) outliers start: 55 outliers final: 37 residues processed: 590 average time/residue: 0.1244 time to fit residues: 110.6761 Evaluate side-chains 563 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 523 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 24 GLN D 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094782 restraints weight = 33988.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098154 restraints weight = 16695.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100217 restraints weight = 10015.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101639 restraints weight = 7076.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102600 restraints weight = 5447.688| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16299 Z= 0.143 Angle : 0.666 17.538 22004 Z= 0.343 Chirality : 0.043 0.215 2348 Planarity : 0.004 0.065 2812 Dihedral : 6.812 57.237 2264 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.74 % Allowed : 26.55 % 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: 1.07 (0.19), residues: 1928 helix: 1.18 (0.15), residues: 1140 sheet: -0.14 (0.41), residues: 134 loop : 0.24 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.023 0.001 TYR C 262 PHE 0.025 0.002 PHE D 259 TRP 0.026 0.002 TRP C 30 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (16298) covalent geometry : angle 0.66585 / 0.34 (22004) hydrogen bonds : bond 0.03943 / 2.51 ( 896) hydrogen bonds : angle 5.12137 / 3.54 ( 2616) Misc. bond : bond 0.00004 / 0.00 ( 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 621 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 574 time to evaluate : 0.473 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 88 LYS cc_start: 0.9198 (tptt) cc_final: 0.8995 (mmmt) REVERT: A 128 PHE cc_start: 0.8886 (t80) cc_final: 0.8626 (t80) REVERT: A 218 ASN cc_start: 0.8821 (t0) cc_final: 0.8528 (t0) REVERT: A 257 ASP cc_start: 0.8668 (m-30) cc_final: 0.8355 (m-30) REVERT: A 286 ASP cc_start: 0.8731 (m-30) cc_final: 0.8516 (m-30) REVERT: A 312 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: A 322 MET cc_start: 0.8218 (tpp) cc_final: 0.7970 (tpp) REVERT: A 350 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7896 (mtp180) REVERT: A 355 TYR cc_start: 0.8157 (m-10) cc_final: 0.7883 (m-10) REVERT: A 379 SER cc_start: 0.9327 (t) cc_final: 0.9022 (t) REVERT: A 383 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8574 (t) REVERT: A 485 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7894 (mtt90) REVERT: A 493 MET cc_start: 0.8916 (tmm) cc_final: 0.8582 (tmm) REVERT: A 560 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8854 (mtmm) REVERT: A 599 GLU cc_start: 0.8329 (mp0) cc_final: 0.8105 (mp0) REVERT: A 640 MET cc_start: 0.8958 (tpp) cc_final: 0.8656 (tpp) REVERT: A 646 GLN cc_start: 0.9065 (mt0) cc_final: 0.8618 (mt0) REVERT: A 684 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: B 31 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: B 65 GLU cc_start: 0.8402 (mp0) cc_final: 0.7528 (mp0) REVERT: B 200 SER cc_start: 0.8890 (t) cc_final: 0.8117 (t) REVERT: B 246 SER cc_start: 0.7574 (m) cc_final: 0.7241 (p) REVERT: B 250 TYR cc_start: 0.9217 (m-80) cc_final: 0.8244 (m-80) REVERT: B 276 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8711 (mmtt) REVERT: B 322 MET cc_start: 0.9055 (mmp) cc_final: 0.8841 (mmt) REVERT: B 344 GLU cc_start: 0.8670 (tt0) cc_final: 0.8406 (tp30) REVERT: B 348 MET cc_start: 0.7667 (tpp) cc_final: 0.7341 (tpp) REVERT: B 379 SER cc_start: 0.8891 (t) cc_final: 0.7643 (t) REVERT: B 394 TYR cc_start: 0.9033 (m-80) cc_final: 0.8778 (m-80) REVERT: B 515 ASP cc_start: 0.8970 (m-30) cc_final: 0.8730 (m-30) REVERT: B 639 ASP cc_start: 0.8499 (m-30) cc_final: 0.7640 (m-30) REVERT: B 640 MET cc_start: 0.9091 (tpp) cc_final: 0.8760 (tpp) REVERT: B 672 LEU cc_start: 0.9326 (mt) cc_final: 0.9104 (mt) REVERT: B 686 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7913 (mtm-85) REVERT: C 56 MET cc_start: -0.4932 (tpt) cc_final: -0.5247 (tpp) REVERT: C 172 PHE cc_start: 0.7571 (m-10) cc_final: 0.7203 (m-80) REVERT: C 178 PHE cc_start: 0.8395 (m-10) cc_final: 0.7941 (m-10) REVERT: C 179 TYR cc_start: 0.8498 (t80) cc_final: 0.8236 (t80) REVERT: C 241 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8358 (mm-30) REVERT: D 18 THR cc_start: 0.6509 (p) cc_final: 0.6205 (p) REVERT: D 20 MET cc_start: 0.8868 (ppp) cc_final: 0.8595 (ppp) REVERT: D 46 TYR cc_start: 0.8783 (m-10) cc_final: 0.8334 (m-80) REVERT: D 120 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8827 (pp20) REVERT: D 174 TYR cc_start: 0.4346 (t80) cc_final: 0.3948 (t80) REVERT: D 204 TYR cc_start: 0.8785 (t80) cc_final: 0.8520 (t80) REVERT: D 211 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8592 (tm-30) REVERT: D 215 LYS cc_start: 0.7265 (mptt) cc_final: 0.7013 (ptmm) REVERT: D 252 LEU cc_start: 0.6607 (mm) cc_final: 0.5925 (mm) REVERT: D 281 ASP cc_start: 0.8473 (p0) cc_final: 0.8235 (t70) outliers start: 47 outliers final: 31 residues processed: 600 average time/residue: 0.1185 time to fit residues: 107.2847 Evaluate side-chains 548 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 513 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 568 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 28 GLN D 234 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.131898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093234 restraints weight = 34403.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096507 restraints weight = 17191.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098689 restraints weight = 10504.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100148 restraints weight = 7358.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101053 restraints weight = 5689.682| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16299 Z= 0.197 Angle : 0.700 20.010 22004 Z= 0.362 Chirality : 0.045 0.333 2348 Planarity : 0.004 0.048 2812 Dihedral : 6.948 56.217 2264 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.21 % Allowed : 28.24 % Favored : 68.55 % 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: 1.10 (0.15), residues: 1129 sheet: -0.50 (0.41), residues: 146 loop : 0.14 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.022 0.002 TYR B 613 PHE 0.036 0.002 PHE B 487 TRP 0.039 0.003 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (16298) covalent geometry : angle 0.69994 / 0.36 (22004) hydrogen bonds : bond 0.04108 / 2.61 ( 896) hydrogen bonds : angle 5.19605 / 3.61 ( 2616) Misc. bond : bond 0.00002 / 0.00 ( 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 588 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 533 time to evaluate : 0.624 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 128 PHE cc_start: 0.8998 (t80) cc_final: 0.8710 (t80) REVERT: A 184 ARG cc_start: 0.8792 (tpp-160) cc_final: 0.8483 (tpp80) REVERT: A 218 ASN cc_start: 0.8891 (t0) cc_final: 0.8633 (t0) REVERT: A 312 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: A 355 TYR cc_start: 0.8168 (m-10) cc_final: 0.7957 (m-10) REVERT: A 383 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8546 (t) REVERT: A 406 ASP cc_start: 0.7983 (m-30) cc_final: 0.7631 (m-30) REVERT: A 485 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7890 (mtt90) REVERT: A 492 PHE cc_start: 0.9113 (m-10) cc_final: 0.8871 (m-10) REVERT: A 493 MET cc_start: 0.8944 (tmm) cc_final: 0.8523 (tmm) REVERT: A 608 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6461 (t0) REVERT: A 646 GLN cc_start: 0.9144 (mt0) cc_final: 0.8652 (mt0) REVERT: A 668 ASN cc_start: 0.8882 (m-40) cc_final: 0.8638 (m-40) REVERT: A 681 THR cc_start: 0.9014 (p) cc_final: 0.8704 (p) REVERT: A 684 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: B 65 GLU cc_start: 0.8444 (mp0) cc_final: 0.7554 (mp0) REVERT: B 116 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8148 (mp0) REVERT: B 200 SER cc_start: 0.8892 (t) cc_final: 0.8129 (t) REVERT: B 246 SER cc_start: 0.7617 (m) cc_final: 0.7304 (p) REVERT: B 250 TYR cc_start: 0.9252 (m-80) cc_final: 0.8276 (m-80) REVERT: B 344 GLU cc_start: 0.8687 (tt0) cc_final: 0.8441 (tp30) REVERT: B 348 MET cc_start: 0.7611 (tpp) cc_final: 0.7268 (tpp) REVERT: B 379 SER cc_start: 0.8911 (t) cc_final: 0.7672 (t) REVERT: B 394 TYR cc_start: 0.9015 (m-80) cc_final: 0.8770 (m-80) REVERT: B 515 ASP cc_start: 0.9026 (m-30) cc_final: 0.8753 (m-30) REVERT: B 586 TYR cc_start: 0.8830 (m-80) cc_final: 0.8469 (m-80) REVERT: B 602 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 672 LEU cc_start: 0.9383 (mt) cc_final: 0.9146 (mt) REVERT: B 686 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7911 (mtm-85) REVERT: C 24 GLN cc_start: 0.8640 (mt0) cc_final: 0.8276 (mm110) REVERT: C 56 MET cc_start: -0.4890 (tpt) cc_final: -0.5268 (tpp) REVERT: C 172 PHE cc_start: 0.7606 (m-10) cc_final: 0.7253 (m-80) REVERT: C 178 PHE cc_start: 0.8393 (m-10) cc_final: 0.7942 (m-10) REVERT: C 179 TYR cc_start: 0.8741 (t80) cc_final: 0.8161 (t80) REVERT: C 185 MET cc_start: 0.5773 (mmm) cc_final: 0.4500 (mpp) REVERT: C 218 GLU cc_start: 0.9104 (mp0) cc_final: 0.8693 (pp20) REVERT: D 18 THR cc_start: 0.6559 (p) cc_final: 0.6300 (p) REVERT: D 179 TYR cc_start: 0.8313 (t80) cc_final: 0.7956 (t80) REVERT: D 204 TYR cc_start: 0.8834 (t80) cc_final: 0.8567 (t80) REVERT: D 211 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8574 (tm-30) REVERT: D 215 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7077 (ptmm) REVERT: D 235 LEU cc_start: 0.9043 (mt) cc_final: 0.8747 (pp) outliers start: 55 outliers final: 37 residues processed: 558 average time/residue: 0.1303 time to fit residues: 109.0676 Evaluate side-chains 552 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 510 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 THR 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: 4.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089752 restraints weight = 35309.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092893 restraints weight = 17650.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094974 restraints weight = 10892.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096338 restraints weight = 7722.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097253 restraints weight = 6063.991| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 16299 Z= 0.306 Angle : 0.788 23.724 22004 Z= 0.409 Chirality : 0.049 0.493 2348 Planarity : 0.004 0.050 2812 Dihedral : 7.295 61.751 2264 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.73 % Allowed : 28.47 % Favored : 67.79 % 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: 0.53 (0.18), residues: 1928 helix: 0.82 (0.15), residues: 1144 sheet: -0.87 (0.40), residues: 152 loop : 0.06 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 196 TYR 0.025 0.002 TYR B 613 PHE 0.051 0.002 PHE D 172 TRP 0.044 0.003 TRP D 124 HIS 0.013 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.31 (16298) covalent geometry : angle 0.78822 / 0.41 (22004) hydrogen bonds : bond 0.04436 / 2.81 ( 896) hydrogen bonds : angle 5.44335 / 3.76 ( 2616) Misc. bond : bond 0.00004 / 0.00 ( 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 558 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 494 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: A 218 ASN cc_start: 0.8952 (t0) cc_final: 0.8697 (t0) REVERT: A 312 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: A 379 SER cc_start: 0.9262 (t) cc_final: 0.8973 (t) REVERT: A 383 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8432 (t) REVERT: A 485 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7659 (mtt90) REVERT: A 493 MET cc_start: 0.8949 (tmm) cc_final: 0.8414 (tmm) REVERT: A 560 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8878 (mtmm) REVERT: A 681 THR cc_start: 0.9061 (p) cc_final: 0.8730 (p) REVERT: A 684 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: B 65 GLU cc_start: 0.8387 (mp0) cc_final: 0.7567 (mp0) REVERT: B 200 SER cc_start: 0.8923 (t) cc_final: 0.8212 (t) REVERT: B 250 TYR cc_start: 0.9271 (m-80) cc_final: 0.8244 (m-80) REVERT: B 276 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8852 (mtmm) REVERT: B 348 MET cc_start: 0.7601 (tpp) cc_final: 0.7222 (tpp) REVERT: B 359 MET cc_start: 0.8946 (ttt) cc_final: 0.8740 (tmm) REVERT: B 379 SER cc_start: 0.8796 (t) cc_final: 0.7851 (t) REVERT: B 452 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: B 515 ASP cc_start: 0.9038 (m-30) cc_final: 0.8732 (m-30) REVERT: B 586 TYR cc_start: 0.8963 (m-80) cc_final: 0.8583 (m-80) REVERT: B 602 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 686 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.7860 (mtm-85) REVERT: C 56 MET cc_start: -0.4926 (tpt) cc_final: -0.5328 (tpp) REVERT: C 137 MET cc_start: 0.3217 (mmm) cc_final: 0.2886 (mmm) REVERT: C 172 PHE cc_start: 0.7829 (m-10) cc_final: 0.7413 (m-10) REVERT: C 178 PHE cc_start: 0.8397 (m-10) cc_final: 0.7970 (m-10) REVERT: C 179 TYR cc_start: 0.8907 (t80) cc_final: 0.8398 (t80) REVERT: C 185 MET cc_start: 0.5764 (mmm) cc_final: 0.4326 (mpp) REVERT: C 218 GLU cc_start: 0.9154 (mp0) cc_final: 0.8719 (pp20) REVERT: D 18 THR cc_start: 0.6527 (p) cc_final: 0.6162 (p) REVERT: D 176 LEU cc_start: 0.9529 (mt) cc_final: 0.9326 (tp) REVERT: D 179 TYR cc_start: 0.8346 (t80) cc_final: 0.8021 (t80) REVERT: D 204 TYR cc_start: 0.8920 (t80) cc_final: 0.8600 (t80) REVERT: D 211 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8568 (tm-30) REVERT: D 215 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7169 (ptmm) REVERT: D 268 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6176 (mp) outliers start: 64 outliers final: 44 residues processed: 518 average time/residue: 0.1236 time to fit residues: 96.2997 Evaluate side-chains 519 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 468 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 311 THR 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: 1.9990 chunk 63 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 210 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093787 restraints weight = 34934.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097113 restraints weight = 17051.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099291 restraints weight = 10312.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100764 restraints weight = 7189.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101640 restraints weight = 5537.396| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16299 Z= 0.154 Angle : 0.738 23.509 22004 Z= 0.379 Chirality : 0.047 0.461 2348 Planarity : 0.004 0.047 2812 Dihedral : 6.902 61.659 2264 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.57 % Allowed : 29.46 % Favored : 67.97 % 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: 0.57 (0.18), residues: 1928 helix: 0.85 (0.15), residues: 1148 sheet: -0.54 (0.43), residues: 130 loop : -0.06 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 196 TYR 0.029 0.002 TYR C 142 PHE 0.039 0.002 PHE D 172 TRP 0.037 0.002 TRP D 124 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16298) covalent geometry : angle 0.73844 / 0.38 (22004) hydrogen bonds : bond 0.04172 / 2.65 ( 896) hydrogen bonds : angle 5.28029 / 3.65 ( 2616) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 533 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7195 (ttm170) REVERT: A 182 ILE cc_start: 0.9329 (mt) cc_final: 0.9070 (mp) REVERT: A 218 ASN cc_start: 0.8894 (t0) cc_final: 0.8656 (t0) REVERT: A 301 PHE cc_start: 0.9104 (m-10) cc_final: 0.8894 (m-10) REVERT: A 312 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: A 383 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8580 (t) REVERT: A 485 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7619 (mtt90) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8145 (tmm) REVERT: A 646 GLN cc_start: 0.9162 (mt0) cc_final: 0.8756 (mt0) REVERT: A 681 THR cc_start: 0.8937 (p) cc_final: 0.8621 (p) REVERT: A 684 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: B 17 MET cc_start: 0.9167 (mmm) cc_final: 0.8841 (mmt) REVERT: B 65 GLU cc_start: 0.8359 (mp0) cc_final: 0.7538 (mp0) REVERT: B 116 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8293 (mp0) REVERT: B 200 SER cc_start: 0.8849 (t) cc_final: 0.8087 (t) REVERT: B 232 ASN cc_start: 0.8961 (t0) cc_final: 0.8591 (m-40) REVERT: B 250 TYR cc_start: 0.9238 (m-80) cc_final: 0.8284 (m-80) REVERT: B 276 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8781 (mtmm) REVERT: B 286 ASP cc_start: 0.8145 (m-30) cc_final: 0.7387 (m-30) REVERT: B 344 GLU cc_start: 0.8685 (tt0) cc_final: 0.8418 (tp30) REVERT: B 348 MET cc_start: 0.7648 (tpp) cc_final: 0.7293 (tpp) REVERT: B 362 ASP cc_start: 0.7953 (m-30) cc_final: 0.6717 (m-30) REVERT: B 379 SER cc_start: 0.8829 (t) cc_final: 0.7801 (t) REVERT: B 452 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7999 (ttm170) REVERT: B 467 ASN cc_start: 0.8952 (m-40) cc_final: 0.8630 (m-40) REVERT: B 515 ASP cc_start: 0.8986 (m-30) cc_final: 0.8607 (m-30) REVERT: B 586 TYR cc_start: 0.8797 (m-80) cc_final: 0.8453 (m-80) REVERT: B 602 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7607 (tm-30) REVERT: B 610 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8525 (mmmm) REVERT: B 639 ASP cc_start: 0.8548 (m-30) cc_final: 0.7753 (m-30) REVERT: B 640 MET cc_start: 0.9157 (tpp) cc_final: 0.8725 (tpp) REVERT: B 686 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.8019 (mtm-85) REVERT: C 23 ASN cc_start: 0.8619 (t0) cc_final: 0.8206 (t0) REVERT: C 24 GLN cc_start: 0.8642 (mt0) cc_final: 0.8204 (mm110) REVERT: C 56 MET cc_start: -0.5026 (tpt) cc_final: -0.5422 (tpp) REVERT: C 172 PHE cc_start: 0.7769 (m-10) cc_final: 0.7371 (m-10) REVERT: C 178 PHE cc_start: 0.8371 (m-10) cc_final: 0.7985 (m-10) REVERT: C 179 TYR cc_start: 0.8834 (t80) cc_final: 0.8383 (t80) REVERT: C 185 MET cc_start: 0.5709 (mmm) cc_final: 0.4443 (mpp) REVERT: C 218 GLU cc_start: 0.9112 (mp0) cc_final: 0.8724 (pp20) REVERT: C 241 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8421 (mm-30) REVERT: D 18 THR cc_start: 0.6543 (p) cc_final: 0.6249 (p) REVERT: D 137 MET cc_start: 0.8528 (mmp) cc_final: 0.7835 (mtp) REVERT: D 142 TYR cc_start: 0.8434 (m-80) cc_final: 0.7989 (t80) REVERT: D 176 LEU cc_start: 0.9512 (mt) cc_final: 0.9261 (tp) REVERT: D 204 TYR cc_start: 0.8964 (t80) cc_final: 0.8598 (t80) REVERT: D 211 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8591 (tm-30) REVERT: D 215 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7093 (ptmm) REVERT: D 266 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7677 (mmmt) REVERT: D 269 MET cc_start: 0.9007 (ptp) cc_final: 0.8783 (ppp) outliers start: 44 outliers final: 31 residues processed: 551 average time/residue: 0.1304 time to fit residues: 107.1554 Evaluate side-chains 537 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 501 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** 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 = 0.3707 r_free = 0.3707 target = 0.131302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092905 restraints weight = 35377.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096163 restraints weight = 17417.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098329 restraints weight = 10544.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099809 restraints weight = 7341.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100752 restraints weight = 5643.225| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16299 Z= 0.185 Angle : 0.768 23.300 22004 Z= 0.397 Chirality : 0.047 0.465 2348 Planarity : 0.004 0.047 2812 Dihedral : 6.963 61.027 2264 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.33 % Allowed : 30.34 % Favored : 67.33 % 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: 0.57 (0.19), residues: 1928 helix: 0.88 (0.15), residues: 1134 sheet: -0.81 (0.41), residues: 146 loop : -0.03 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 196 TYR 0.027 0.002 TYR D 174 PHE 0.040 0.002 PHE D 172 TRP 0.054 0.003 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (16298) covalent geometry : angle 0.76834 / 0.40 (22004) hydrogen bonds : bond 0.04247 / 2.69 ( 896) hydrogen bonds : angle 5.34719 / 3.71 ( 2616) Misc. bond : bond 0.00013 / 0.01 ( 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 541 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 501 time to evaluate : 0.714 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: A 161 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7187 (ttm170) REVERT: A 182 ILE cc_start: 0.9320 (mt) cc_final: 0.9057 (mp) REVERT: A 218 ASN cc_start: 0.8908 (t0) cc_final: 0.8668 (t0) REVERT: A 312 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: A 350 ARG cc_start: 0.8223 (mtp180) cc_final: 0.8002 (mtp180) REVERT: A 383 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 485 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7886 (mtt90) REVERT: A 492 PHE cc_start: 0.9131 (m-10) cc_final: 0.8909 (m-10) REVERT: A 493 MET cc_start: 0.8945 (tmm) cc_final: 0.8525 (tmm) REVERT: A 608 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6522 (t0) REVERT: A 646 GLN cc_start: 0.9181 (mt0) cc_final: 0.8840 (mt0) REVERT: A 681 THR cc_start: 0.8935 (p) cc_final: 0.8603 (p) REVERT: A 684 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: B 17 MET cc_start: 0.9091 (mmm) cc_final: 0.8783 (mmt) REVERT: B 65 GLU cc_start: 0.8344 (mp0) cc_final: 0.7534 (mp0) REVERT: B 116 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8073 (mp0) REVERT: B 161 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7471 (mtt180) REVERT: B 200 SER cc_start: 0.8861 (t) cc_final: 0.8132 (t) REVERT: B 235 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8232 (ttm-80) REVERT: B 250 TYR cc_start: 0.9251 (m-80) cc_final: 0.8297 (m-80) REVERT: B 276 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8778 (mtmm) REVERT: B 286 ASP cc_start: 0.8110 (m-30) cc_final: 0.7380 (m-30) REVERT: B 344 GLU cc_start: 0.8705 (tt0) cc_final: 0.8435 (tp30) REVERT: B 348 MET cc_start: 0.7673 (tpp) cc_final: 0.7310 (tpp) REVERT: B 362 ASP cc_start: 0.7938 (m-30) cc_final: 0.6725 (m-30) REVERT: B 379 SER cc_start: 0.8717 (t) cc_final: 0.7720 (t) REVERT: B 452 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: B 467 ASN cc_start: 0.8991 (m-40) cc_final: 0.8787 (m-40) REVERT: B 515 ASP cc_start: 0.8946 (m-30) cc_final: 0.8534 (m-30) REVERT: B 586 TYR cc_start: 0.8794 (m-80) cc_final: 0.8233 (m-80) REVERT: B 602 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 610 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8526 (mmmm) REVERT: B 640 MET cc_start: 0.9165 (tpp) cc_final: 0.8835 (tpp) REVERT: B 672 LEU cc_start: 0.9414 (mt) cc_final: 0.9174 (mt) REVERT: B 686 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8012 (mtm-85) REVERT: C 23 ASN cc_start: 0.8617 (t0) cc_final: 0.8193 (t0) REVERT: C 24 GLN cc_start: 0.8645 (mt0) cc_final: 0.8190 (mm110) REVERT: C 56 MET cc_start: -0.5034 (tpt) cc_final: -0.5421 (tpp) REVERT: C 172 PHE cc_start: 0.7796 (m-10) cc_final: 0.7382 (m-10) REVERT: C 178 PHE cc_start: 0.8412 (m-10) cc_final: 0.8058 (m-10) REVERT: C 179 TYR cc_start: 0.8869 (t80) cc_final: 0.8411 (t80) REVERT: C 185 MET cc_start: 0.5606 (mmm) cc_final: 0.4396 (mpp) REVERT: C 218 GLU cc_start: 0.9136 (mp0) cc_final: 0.8754 (pp20) REVERT: D 18 THR cc_start: 0.6536 (p) cc_final: 0.6281 (p) REVERT: D 74 MET cc_start: 0.6320 (tmm) cc_final: 0.5212 (ppp) REVERT: D 137 MET cc_start: 0.8576 (mmp) cc_final: 0.7946 (mtp) REVERT: D 142 TYR cc_start: 0.8383 (m-80) cc_final: 0.7933 (t80) REVERT: D 176 LEU cc_start: 0.9509 (mt) cc_final: 0.9269 (tp) REVERT: D 204 TYR cc_start: 0.8935 (t80) cc_final: 0.8590 (t80) REVERT: D 266 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7708 (mmmt) REVERT: D 269 MET cc_start: 0.9085 (ptp) cc_final: 0.8786 (ppp) outliers start: 40 outliers final: 32 residues processed: 518 average time/residue: 0.1251 time to fit residues: 96.4115 Evaluate side-chains 523 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 486 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN B 43 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094651 restraints weight = 35133.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097982 restraints weight = 17235.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100100 restraints weight = 10434.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101631 restraints weight = 7349.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102580 restraints weight = 5646.643| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16299 Z= 0.156 Angle : 0.759 23.154 22004 Z= 0.390 Chirality : 0.047 0.457 2348 Planarity : 0.004 0.047 2812 Dihedral : 6.809 60.975 2264 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.22 % Allowed : 30.86 % Favored : 66.92 % 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: 0.54 (0.19), residues: 1928 helix: 0.86 (0.15), residues: 1135 sheet: -0.61 (0.43), residues: 134 loop : -0.10 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.036 0.001 TYR C 142 PHE 0.042 0.002 PHE B 487 TRP 0.054 0.003 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (16298) covalent geometry : angle 0.75917 / 0.39 (22004) hydrogen bonds : bond 0.04172 / 2.63 ( 896) hydrogen bonds : angle 5.27592 / 3.66 ( 2616) Misc. bond : bond 0.00010 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3240.02 seconds wall clock time: 56 minutes 52.86 seconds (3412.86 seconds total)