Starting phenix.real_space_refine on Thu Aug 6 14:48:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx2_44991/08_2026/9bx2_44991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx2_44991/08_2026/9bx2_44991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx2_44991/08_2026/9bx2_44991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx2_44991/08_2026/9bx2_44991.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx2_44991/08_2026/9bx2_44991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx2_44991/08_2026/9bx2_44991_neut.cif" } resolution = 3.79 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: 3.60, per 1000 atoms: 0.23 Number of scatterers: 15954 At special positions: 0 Unit cell: (95.046, 140.014, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 585.3 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: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.075A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A 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: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.621A 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: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.565A 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: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A 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: 3.736A 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: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.793A 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: 2.98 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4844 1.33 - 1.46: 2960 1.46 - 1.58: 8319 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 4.95e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.90e+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 1.13e+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 1.12e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21460 2.10 - 4.21: 471 4.21 - 6.31: 58 6.31 - 8.42: 8 8.42 - 10.52: 7 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+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=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.71 10.52 3.00e+00 1.11e-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 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8646 17.66 - 35.32: 852 35.32 - 52.98: 254 52.98 - 70.64: 64 70.64 - 88.30: 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 -134.38 12.38 0 2.50e+00 1.60e-01 2.45e+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 123.40 135.59 -12.19 0 2.50e+00 1.60e-01 2.38e+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 -134.32 11.72 0 2.50e+00 1.60e-01 2.20e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2126 0.094 - 0.187: 182 0.187 - 0.281: 33 0.281 - 0.374: 5 0.374 - 0.468: 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 5.47e+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 4.66e+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 2.92e+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 5.52e-02 4.88e+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 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.11e+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 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11872 3.11 - 3.70: 26434 3.70 - 4.30: 41217 4.30 - 4.90: 64993 Nonbonded interactions: 144648 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 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144643 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: 0.03 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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= 0.733 Angle : 0.756 10.524 22004 Z= 0.462 Chirality : 0.059 0.468 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.904 88.298 6168 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 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 0.75633 / 0.46 (22004) hydrogen bonds : bond 0.16169 / 10.53 ( 896) hydrogen bonds : angle 6.35147 / 4.47 ( 2616) Misc. bond : bond 0.83443 / 43.92 ( 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 910 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 886 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.7919 (m-80) cc_final: 0.7670 (m-80) REVERT: A 101 TYR cc_start: 0.8052 (m-80) cc_final: 0.7846 (m-80) REVERT: A 147 GLN cc_start: 0.8560 (mt0) cc_final: 0.7467 (mt0) REVERT: A 152 SER cc_start: 0.8560 (p) cc_final: 0.8218 (p) REVERT: A 179 LEU cc_start: 0.9405 (tp) cc_final: 0.9188 (tp) REVERT: A 181 ASP cc_start: 0.8156 (m-30) cc_final: 0.7915 (m-30) REVERT: A 188 ILE cc_start: 0.9049 (mt) cc_final: 0.8829 (mt) REVERT: A 232 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7971 (m-40) REVERT: A 246 SER cc_start: 0.8278 (m) cc_final: 0.8039 (p) REVERT: A 406 ASP cc_start: 0.7400 (m-30) cc_final: 0.7190 (m-30) REVERT: A 411 LEU cc_start: 0.8475 (mt) cc_final: 0.8056 (mp) REVERT: A 442 THR cc_start: 0.8764 (p) cc_final: 0.8349 (m) REVERT: A 583 SER cc_start: 0.8154 (m) cc_final: 0.7926 (t) REVERT: B 104 TYR cc_start: 0.7704 (m-80) cc_final: 0.7393 (m-80) REVERT: B 116 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 172 LEU cc_start: 0.9028 (mp) cc_final: 0.8479 (mp) REVERT: B 181 ASP cc_start: 0.8382 (m-30) cc_final: 0.7907 (m-30) REVERT: B 227 MET cc_start: 0.7932 (mtp) cc_final: 0.7487 (mtp) REVERT: B 267 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7823 (pt) REVERT: B 276 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8225 (mtmm) REVERT: B 280 ILE cc_start: 0.9081 (pt) cc_final: 0.8833 (pt) REVERT: B 294 GLU cc_start: 0.6773 (mt-10) cc_final: 0.4936 (mt-10) REVERT: B 358 ILE cc_start: 0.9388 (mm) cc_final: 0.9164 (mm) REVERT: B 375 LYS cc_start: 0.9185 (mptp) cc_final: 0.8940 (mmtp) REVERT: B 396 ASP cc_start: 0.7618 (m-30) cc_final: 0.7396 (m-30) REVERT: B 550 MET cc_start: 0.8110 (ttm) cc_final: 0.7665 (mtp) REVERT: B 583 SER cc_start: 0.8125 (m) cc_final: 0.7778 (t) REVERT: B 597 ILE cc_start: 0.9145 (pt) cc_final: 0.8926 (pt) REVERT: B 637 VAL cc_start: 0.9061 (t) cc_final: 0.8850 (t) REVERT: C 26 VAL cc_start: 0.7638 (m) cc_final: 0.7122 (m) REVERT: C 106 SER cc_start: 0.7849 (m) cc_final: 0.7089 (t) REVERT: C 153 LEU cc_start: 0.6349 (tp) cc_final: 0.5530 (tp) REVERT: C 229 ILE cc_start: 0.3543 (mt) cc_final: 0.3299 (mt) REVERT: C 316 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7776 (mtmm) REVERT: D 55 TYR cc_start: 0.5619 (t80) cc_final: 0.5408 (t80) REVERT: D 96 MET cc_start: 0.5853 (mmm) cc_final: 0.5391 (mmm) REVERT: D 178 PHE cc_start: 0.6543 (m-80) cc_final: 0.5485 (m-10) REVERT: D 256 VAL cc_start: 0.6468 (t) cc_final: 0.6261 (p) outliers start: 24 outliers final: 4 residues processed: 894 average time/residue: 0.1154 time to fit residues: 152.2923 Evaluate side-chains 547 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 540 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 14 ASN A 49 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 14 ASN B 232 ASN B 312 GLN B 474 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 25 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 283 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 80 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.090481 restraints weight = 32056.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.093636 restraints weight = 15175.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095761 restraints weight = 9189.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.097143 restraints weight = 6458.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098053 restraints weight = 5035.919| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16299 Z= 0.253 Angle : 0.700 9.822 22004 Z= 0.374 Chirality : 0.046 0.185 2348 Planarity : 0.004 0.053 2812 Dihedral : 7.197 64.429 2280 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.08 % Allowed : 17.91 % Favored : 78.00 % 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: 1.60 (0.19), residues: 1928 helix: 1.46 (0.15), residues: 1133 sheet: 0.36 (0.40), residues: 134 loop : 0.75 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.036 0.002 TYR D 262 PHE 0.025 0.002 PHE C 122 TRP 0.027 0.003 TRP C 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (16298) covalent geometry : angle 0.69997 / 0.37 (22004) hydrogen bonds : bond 0.05027 / 3.18 ( 896) hydrogen bonds : angle 5.25879 / 3.67 ( 2616) Misc. bond : bond 0.00213 / 0.11 ( 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 644 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 574 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.9402 (tp) cc_final: 0.9144 (tp) REVERT: A 147 GLN cc_start: 0.9450 (mt0) cc_final: 0.9219 (mt0) REVERT: A 157 LEU cc_start: 0.9155 (tt) cc_final: 0.8736 (tp) REVERT: A 174 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 181 ASP cc_start: 0.8757 (m-30) cc_final: 0.8497 (m-30) REVERT: A 214 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8359 (mmtm) REVERT: A 232 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8455 (m110) REVERT: A 246 SER cc_start: 0.7466 (m) cc_final: 0.7178 (p) REVERT: A 256 ARG cc_start: 0.8914 (tpt90) cc_final: 0.8653 (tpt90) REVERT: A 348 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (tmm) REVERT: A 393 SER cc_start: 0.8770 (m) cc_final: 0.8478 (p) REVERT: A 446 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7527 (mmp-170) REVERT: A 509 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 583 SER cc_start: 0.8784 (m) cc_final: 0.8320 (t) REVERT: A 598 MET cc_start: 0.8068 (mtp) cc_final: 0.7715 (mtp) REVERT: A 599 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: A 658 LEU cc_start: 0.9568 (mp) cc_final: 0.9303 (mt) REVERT: A 686 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7510 (mtp85) REVERT: B 64 TYR cc_start: 0.8645 (m-10) cc_final: 0.8418 (m-10) REVERT: B 102 ASN cc_start: 0.9296 (m-40) cc_final: 0.8836 (m110) REVERT: B 109 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9031 (m110) REVERT: B 172 LEU cc_start: 0.8874 (mp) cc_final: 0.8660 (mp) REVERT: B 184 ARG cc_start: 0.9126 (tpp-160) cc_final: 0.8848 (tpp80) REVERT: B 317 MET cc_start: 0.8586 (mtm) cc_final: 0.8275 (mtt) REVERT: B 334 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8945 (ptpt) REVERT: B 466 MET cc_start: 0.8962 (ptt) cc_final: 0.8746 (ptp) REVERT: B 515 ASP cc_start: 0.9078 (m-30) cc_final: 0.8857 (m-30) REVERT: B 550 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7749 (mtp) REVERT: B 583 SER cc_start: 0.8935 (m) cc_final: 0.8671 (t) REVERT: B 599 GLU cc_start: 0.8703 (pt0) cc_final: 0.8490 (pm20) REVERT: B 602 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: B 604 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8701 (mmm160) REVERT: C 20 MET cc_start: 0.9341 (mpp) cc_final: 0.8552 (tmm) REVERT: C 26 VAL cc_start: 0.9434 (m) cc_final: 0.9078 (m) REVERT: C 29 PHE cc_start: 0.6952 (p90) cc_final: 0.6655 (p90) REVERT: C 30 TRP cc_start: 0.7296 (p-90) cc_final: 0.7050 (p-90) REVERT: C 89 VAL cc_start: 0.8274 (t) cc_final: 0.7807 (t) REVERT: C 92 PHE cc_start: 0.9058 (t80) cc_final: 0.8764 (t80) REVERT: C 96 MET cc_start: 0.8092 (mmm) cc_final: 0.7697 (mmm) REVERT: C 118 ILE cc_start: 0.8525 (mt) cc_final: 0.7977 (pt) REVERT: C 124 TRP cc_start: 0.7641 (t60) cc_final: 0.7192 (t60) REVERT: C 162 TYR cc_start: 0.8836 (m-10) cc_final: 0.8364 (m-80) REVERT: C 212 ILE cc_start: 0.7215 (mm) cc_final: 0.6699 (mm) REVERT: C 229 ILE cc_start: 0.5193 (mt) cc_final: 0.4975 (mt) REVERT: D 20 MET cc_start: 0.9368 (mmm) cc_final: 0.8891 (ptm) REVERT: D 21 PHE cc_start: 0.8317 (m-80) cc_final: 0.7989 (m-10) REVERT: D 25 ASN cc_start: 0.9499 (m-40) cc_final: 0.9225 (m-40) REVERT: D 30 TRP cc_start: 0.8013 (p-90) cc_final: 0.7219 (p-90) REVERT: D 76 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8153 (mt) REVERT: D 96 MET cc_start: 0.7563 (mmm) cc_final: 0.7201 (mmm) REVERT: D 162 TYR cc_start: 0.9020 (m-10) cc_final: 0.8741 (m-80) REVERT: D 178 PHE cc_start: 0.8747 (m-10) cc_final: 0.7992 (m-10) REVERT: D 227 PHE cc_start: 0.7852 (m-10) cc_final: 0.7598 (m-80) REVERT: D 259 PHE cc_start: 0.8359 (t80) cc_final: 0.8119 (t80) REVERT: D 265 ASN cc_start: 0.7339 (m110) cc_final: 0.7120 (m110) REVERT: D 273 PHE cc_start: 0.6701 (m-80) cc_final: 0.6212 (t80) REVERT: D 320 PHE cc_start: 0.8663 (m-80) cc_final: 0.8342 (m-80) outliers start: 70 outliers final: 37 residues processed: 612 average time/residue: 0.1046 time to fit residues: 96.4685 Evaluate side-chains 540 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 495 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL 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: 4.9990 chunk 181 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 645 GLN C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.090322 restraints weight = 32260.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.093465 restraints weight = 15071.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.095585 restraints weight = 9112.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096955 restraints weight = 6339.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.097833 restraints weight = 4967.621| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4633 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= 0.201 Angle : 0.653 9.400 22004 Z= 0.342 Chirality : 0.044 0.178 2348 Planarity : 0.004 0.050 2812 Dihedral : 7.147 61.126 2270 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.68 % Allowed : 19.43 % Favored : 76.90 % 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: 1.45 (0.18), residues: 1928 helix: 1.34 (0.15), residues: 1130 sheet: 0.14 (0.41), residues: 134 loop : 0.71 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.038 0.002 TYR D 142 PHE 0.028 0.002 PHE C 122 TRP 0.019 0.002 TRP C 44 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (16298) covalent geometry : angle 0.65306 / 0.34 (22004) hydrogen bonds : bond 0.04448 / 2.81 ( 896) hydrogen bonds : angle 5.09121 / 3.57 ( 2616) Misc. bond : bond 0.00131 / 0.07 ( 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 612 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 549 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8957 (mp) cc_final: 0.8511 (mp) REVERT: A 139 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8352 (mm-30) REVERT: A 143 LEU cc_start: 0.9397 (tp) cc_final: 0.9133 (tp) REVERT: A 147 GLN cc_start: 0.9357 (mt0) cc_final: 0.9126 (mt0) REVERT: A 150 GLN cc_start: 0.8525 (tp40) cc_final: 0.8009 (tp40) REVERT: A 157 LEU cc_start: 0.9263 (tt) cc_final: 0.8987 (tp) REVERT: A 161 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7540 (mtm-85) REVERT: A 174 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 181 ASP cc_start: 0.8743 (m-30) cc_final: 0.8529 (m-30) REVERT: A 214 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8406 (mmtm) REVERT: A 232 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8450 (m-40) REVERT: A 286 ASP cc_start: 0.8134 (m-30) cc_final: 0.7767 (m-30) REVERT: A 334 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8434 (ptpt) REVERT: A 348 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8522 (tmm) REVERT: A 362 ASP cc_start: 0.8391 (m-30) cc_final: 0.7763 (m-30) REVERT: A 383 SER cc_start: 0.8937 (m) cc_final: 0.8564 (t) REVERT: A 393 SER cc_start: 0.8857 (m) cc_final: 0.8578 (p) REVERT: A 509 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 598 MET cc_start: 0.8112 (mtp) cc_final: 0.6763 (mtp) REVERT: A 599 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: A 658 LEU cc_start: 0.9534 (mp) cc_final: 0.9293 (mt) REVERT: B 102 ASN cc_start: 0.9286 (m-40) cc_final: 0.8860 (m110) REVERT: B 104 TYR cc_start: 0.8936 (m-80) cc_final: 0.8512 (m-80) REVERT: B 109 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.9029 (m-40) REVERT: B 121 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.9170 (tpt170) REVERT: B 172 LEU cc_start: 0.8956 (mp) cc_final: 0.8414 (mp) REVERT: B 184 ARG cc_start: 0.9140 (tpp-160) cc_final: 0.8852 (tpp80) REVERT: B 238 ASP cc_start: 0.7925 (t0) cc_final: 0.7191 (t70) REVERT: B 334 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8799 (ptpt) REVERT: B 381 LEU cc_start: 0.9368 (tt) cc_final: 0.9136 (tp) REVERT: B 415 ASN cc_start: 0.9153 (t0) cc_final: 0.8862 (t0) REVERT: B 515 ASP cc_start: 0.9092 (m-30) cc_final: 0.8837 (m-30) REVERT: B 550 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8033 (mtp) REVERT: B 570 MET cc_start: 0.8531 (mtp) cc_final: 0.8307 (mtp) REVERT: B 599 GLU cc_start: 0.8717 (pt0) cc_final: 0.7771 (pm20) REVERT: B 602 GLU cc_start: 0.8600 (tt0) cc_final: 0.7706 (tp30) REVERT: B 604 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8360 (mmm160) REVERT: B 639 ASP cc_start: 0.8419 (m-30) cc_final: 0.8115 (m-30) REVERT: C 20 MET cc_start: 0.9538 (mpp) cc_final: 0.9255 (ppp) REVERT: C 26 VAL cc_start: 0.9362 (m) cc_final: 0.9042 (m) REVERT: C 29 PHE cc_start: 0.6918 (p90) cc_final: 0.6709 (p90) REVERT: C 89 VAL cc_start: 0.8396 (t) cc_final: 0.8120 (t) REVERT: C 93 MET cc_start: 0.8730 (mtt) cc_final: 0.8096 (mtt) REVERT: C 95 MET cc_start: 0.8784 (tmm) cc_final: 0.8286 (tmm) REVERT: C 96 MET cc_start: 0.8218 (mmm) cc_final: 0.7382 (mmm) REVERT: C 109 PHE cc_start: 0.8398 (m-10) cc_final: 0.8105 (m-80) REVERT: C 118 ILE cc_start: 0.8323 (mt) cc_final: 0.8109 (pt) REVERT: C 124 TRP cc_start: 0.7901 (t60) cc_final: 0.7275 (t60) REVERT: C 129 LYS cc_start: 0.9423 (mmmt) cc_final: 0.8949 (mmmt) REVERT: C 162 TYR cc_start: 0.8835 (m-10) cc_final: 0.8296 (m-80) REVERT: C 178 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: C 197 ASP cc_start: 0.8542 (t70) cc_final: 0.8336 (t70) REVERT: D 21 PHE cc_start: 0.8398 (m-80) cc_final: 0.8091 (m-10) REVERT: D 25 ASN cc_start: 0.9636 (m-40) cc_final: 0.9373 (m-40) REVERT: D 56 MET cc_start: 0.8538 (ptt) cc_final: 0.8306 (mmp) REVERT: D 96 MET cc_start: 0.7430 (mmm) cc_final: 0.7050 (mmm) REVERT: D 110 MET cc_start: 0.8806 (ppp) cc_final: 0.8598 (ppp) REVERT: D 174 TYR cc_start: 0.8647 (t80) cc_final: 0.8406 (t80) REVERT: D 178 PHE cc_start: 0.8624 (m-10) cc_final: 0.8400 (m-10) REVERT: D 213 TYR cc_start: 0.6938 (t80) cc_final: 0.6614 (t80) REVERT: D 227 PHE cc_start: 0.7827 (m-10) cc_final: 0.7506 (m-80) outliers start: 63 outliers final: 39 residues processed: 581 average time/residue: 0.1139 time to fit residues: 98.7347 Evaluate side-chains 554 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 505 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.088099 restraints weight = 32792.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091218 restraints weight = 15353.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.093235 restraints weight = 9125.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.094468 restraints weight = 6444.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095410 restraints weight = 5112.834| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16299 Z= 0.231 Angle : 0.649 9.251 22004 Z= 0.339 Chirality : 0.044 0.203 2348 Planarity : 0.004 0.048 2812 Dihedral : 7.023 60.994 2268 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.61 % Allowed : 19.25 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 1928 helix: 1.27 (0.15), residues: 1127 sheet: -0.20 (0.40), residues: 142 loop : 0.60 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 196 TYR 0.038 0.002 TYR D 142 PHE 0.055 0.002 PHE C 122 TRP 0.025 0.003 TRP D 30 HIS 0.017 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (16298) covalent geometry : angle 0.64855 / 0.34 (22004) hydrogen bonds : bond 0.04236 / 2.69 ( 896) hydrogen bonds : angle 5.03716 / 3.54 ( 2616) Misc. bond : bond 0.00058 / 0.03 ( 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 607 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 528 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 147 GLN cc_start: 0.9316 (mt0) cc_final: 0.9060 (mt0) REVERT: A 150 GLN cc_start: 0.8586 (tp40) cc_final: 0.8035 (tp40) REVERT: A 157 LEU cc_start: 0.9183 (tt) cc_final: 0.8863 (tp) REVERT: A 161 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7639 (mtm-85) REVERT: A 174 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 191 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8474 (mm-40) REVERT: A 214 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8404 (mmtm) REVERT: A 232 ASN cc_start: 0.9128 (m-40) cc_final: 0.8433 (m110) REVERT: A 286 ASP cc_start: 0.8159 (m-30) cc_final: 0.7849 (m-30) REVERT: A 334 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8364 (ptpt) REVERT: A 335 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 348 MET cc_start: 0.8862 (ttp) cc_final: 0.8547 (tmm) REVERT: A 362 ASP cc_start: 0.8486 (m-30) cc_final: 0.7546 (m-30) REVERT: A 383 SER cc_start: 0.8903 (m) cc_final: 0.8687 (t) REVERT: A 393 SER cc_start: 0.8904 (m) cc_final: 0.8251 (p) REVERT: A 415 ASN cc_start: 0.9169 (t0) cc_final: 0.8968 (t0) REVERT: A 492 PHE cc_start: 0.9466 (m-80) cc_final: 0.9260 (m-80) REVERT: A 598 MET cc_start: 0.8200 (mtp) cc_final: 0.6988 (mtp) REVERT: A 599 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7898 (pt0) REVERT: A 602 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: A 604 ARG cc_start: 0.8540 (mtp85) cc_final: 0.7943 (mmp80) REVERT: A 686 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6912 (mtp85) REVERT: B 52 LYS cc_start: 0.9216 (tppt) cc_final: 0.8772 (tppt) REVERT: B 56 ASP cc_start: 0.8950 (m-30) cc_final: 0.8702 (m-30) REVERT: B 78 LYS cc_start: 0.9187 (pttm) cc_final: 0.8973 (pttp) REVERT: B 95 MET cc_start: 0.9240 (tpp) cc_final: 0.9005 (tpp) REVERT: B 102 ASN cc_start: 0.9288 (m-40) cc_final: 0.8869 (m110) REVERT: B 104 TYR cc_start: 0.9030 (m-80) cc_final: 0.8672 (m-80) REVERT: B 121 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.9198 (tpt170) REVERT: B 172 LEU cc_start: 0.8939 (mp) cc_final: 0.8694 (mp) REVERT: B 184 ARG cc_start: 0.9160 (tpp-160) cc_final: 0.8865 (tpp80) REVERT: B 238 ASP cc_start: 0.7940 (t0) cc_final: 0.7117 (t0) REVERT: B 317 MET cc_start: 0.8641 (mtm) cc_final: 0.8354 (mtt) REVERT: B 334 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8755 (ptpt) REVERT: B 515 ASP cc_start: 0.9105 (m-30) cc_final: 0.8892 (m-30) REVERT: B 550 MET cc_start: 0.8234 (ttm) cc_final: 0.7928 (mtp) REVERT: B 599 GLU cc_start: 0.8597 (pt0) cc_final: 0.7106 (pm20) REVERT: B 610 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8174 (mmmt) REVERT: B 639 ASP cc_start: 0.8441 (m-30) cc_final: 0.8061 (m-30) REVERT: C 17 PHE cc_start: 0.7960 (p90) cc_final: 0.6910 (p90) REVERT: C 26 VAL cc_start: 0.9353 (m) cc_final: 0.9032 (m) REVERT: C 43 THR cc_start: 0.0344 (OUTLIER) cc_final: -0.0173 (p) REVERT: C 89 VAL cc_start: 0.8425 (t) cc_final: 0.8156 (t) REVERT: C 92 PHE cc_start: 0.9259 (t80) cc_final: 0.8687 (t80) REVERT: C 95 MET cc_start: 0.8848 (tmm) cc_final: 0.8153 (tmm) REVERT: C 96 MET cc_start: 0.8383 (mmm) cc_final: 0.7442 (mmm) REVERT: C 109 PHE cc_start: 0.8363 (m-10) cc_final: 0.8031 (m-80) REVERT: C 162 TYR cc_start: 0.8850 (m-10) cc_final: 0.8198 (m-10) REVERT: C 178 PHE cc_start: 0.7983 (m-10) cc_final: 0.7478 (m-10) REVERT: C 185 MET cc_start: 0.3536 (mpp) cc_final: 0.3074 (mmm) REVERT: C 271 LEU cc_start: 0.8540 (mt) cc_final: 0.8278 (mt) REVERT: D 20 MET cc_start: 0.9457 (mmm) cc_final: 0.9031 (ptm) REVERT: D 25 ASN cc_start: 0.9592 (m-40) cc_final: 0.9371 (m-40) REVERT: D 109 PHE cc_start: 0.8353 (m-80) cc_final: 0.7992 (m-80) REVERT: D 134 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7286 (pttt) REVERT: D 154 PHE cc_start: 0.8220 (t80) cc_final: 0.7946 (t80) REVERT: D 162 TYR cc_start: 0.8831 (m-80) cc_final: 0.8507 (m-10) REVERT: D 174 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8574 (t80) REVERT: D 178 PHE cc_start: 0.8586 (m-10) cc_final: 0.8294 (m-10) REVERT: D 213 TYR cc_start: 0.6878 (t80) cc_final: 0.6616 (t80) REVERT: D 227 PHE cc_start: 0.8128 (m-10) cc_final: 0.7754 (m-80) REVERT: D 240 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6612 (pp) REVERT: D 246 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6581 (mm) outliers start: 79 outliers final: 48 residues processed: 571 average time/residue: 0.1075 time to fit residues: 92.6183 Evaluate side-chains 554 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 495 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 0.0030 chunk 33 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 249 GLN D 80 HIS D 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.092864 restraints weight = 32463.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096122 restraints weight = 14989.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098144 restraints weight = 8789.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099481 restraints weight = 6142.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100323 restraints weight = 4779.072| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (14 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16299 Z= 0.131 Angle : 0.624 10.162 22004 Z= 0.321 Chirality : 0.043 0.181 2348 Planarity : 0.004 0.046 2812 Dihedral : 6.636 61.117 2265 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.21 % Allowed : 21.94 % Favored : 74.85 % 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: 1.28 (0.19), residues: 1928 helix: 1.22 (0.15), residues: 1143 sheet: 0.57 (0.46), residues: 108 loop : 0.46 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.038 0.002 TYR D 142 PHE 0.038 0.002 PHE D 168 TRP 0.027 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16298) covalent geometry : angle 0.62361 / 0.32 (22004) hydrogen bonds : bond 0.03952 / 2.49 ( 896) hydrogen bonds : angle 4.96241 / 3.48 ( 2616) Misc. bond : bond 0.00046 / 0.02 ( 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 596 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 541 time to evaluate : 0.591 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 115 LEU cc_start: 0.8961 (mp) cc_final: 0.8304 (mt) REVERT: A 119 GLU cc_start: 0.8470 (mp0) cc_final: 0.7956 (mp0) REVERT: A 135 GLU cc_start: 0.8600 (mp0) cc_final: 0.8388 (mp0) REVERT: A 139 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 164 ARG cc_start: 0.8338 (ptt90) cc_final: 0.7936 (ptm-80) REVERT: A 174 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 191 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8309 (mm-40) REVERT: A 214 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8252 (mmtm) REVERT: A 232 ASN cc_start: 0.9073 (m-40) cc_final: 0.8419 (m110) REVERT: A 256 ARG cc_start: 0.8970 (tpt90) cc_final: 0.8401 (tpt90) REVERT: A 317 MET cc_start: 0.8403 (mtt) cc_final: 0.8119 (mtt) REVERT: A 348 MET cc_start: 0.8834 (ttp) cc_final: 0.8539 (tmm) REVERT: A 362 ASP cc_start: 0.8430 (m-30) cc_final: 0.7564 (m-30) REVERT: A 383 SER cc_start: 0.8768 (m) cc_final: 0.8509 (t) REVERT: A 393 SER cc_start: 0.8840 (m) cc_final: 0.8330 (p) REVERT: A 415 ASN cc_start: 0.9121 (t0) cc_final: 0.8908 (t0) REVERT: A 446 ARG cc_start: 0.7816 (mmp80) cc_final: 0.7174 (mmp-170) REVERT: A 598 MET cc_start: 0.8274 (mtp) cc_final: 0.8036 (mtp) REVERT: A 599 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: A 602 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: A 604 ARG cc_start: 0.8487 (mtp85) cc_final: 0.7895 (mmp80) REVERT: A 612 TYR cc_start: 0.8871 (m-80) cc_final: 0.8660 (m-80) REVERT: B 52 LYS cc_start: 0.9172 (tppt) cc_final: 0.8703 (tppt) REVERT: B 56 ASP cc_start: 0.9013 (m-30) cc_final: 0.8714 (m-30) REVERT: B 78 LYS cc_start: 0.9187 (pttm) cc_final: 0.8934 (pttp) REVERT: B 95 MET cc_start: 0.9171 (tpp) cc_final: 0.8893 (tpp) REVERT: B 102 ASN cc_start: 0.9258 (m-40) cc_final: 0.8888 (m110) REVERT: B 104 TYR cc_start: 0.8894 (m-80) cc_final: 0.8446 (m-80) REVERT: B 147 GLN cc_start: 0.9363 (mt0) cc_final: 0.8978 (mm110) REVERT: B 172 LEU cc_start: 0.8874 (mp) cc_final: 0.8583 (mp) REVERT: B 184 ARG cc_start: 0.9133 (tpp-160) cc_final: 0.8863 (tpp80) REVERT: B 235 ARG cc_start: 0.8746 (ttp-110) cc_final: 0.8302 (ttm110) REVERT: B 238 ASP cc_start: 0.7904 (t0) cc_final: 0.7207 (t70) REVERT: B 357 TYR cc_start: 0.8787 (m-10) cc_final: 0.8362 (m-10) REVERT: B 474 GLN cc_start: 0.8674 (mt0) cc_final: 0.8426 (mt0) REVERT: B 515 ASP cc_start: 0.9061 (m-30) cc_final: 0.8798 (m-30) REVERT: B 586 TYR cc_start: 0.9165 (m-80) cc_final: 0.8610 (m-80) REVERT: B 639 ASP cc_start: 0.8534 (m-30) cc_final: 0.8098 (m-30) REVERT: B 686 ARG cc_start: 0.8017 (mmt180) cc_final: 0.7776 (mmt180) REVERT: C 17 PHE cc_start: 0.7633 (p90) cc_final: 0.7385 (p90) REVERT: C 30 TRP cc_start: 0.6939 (p-90) cc_final: 0.6048 (p-90) REVERT: C 92 PHE cc_start: 0.9370 (t80) cc_final: 0.8878 (t80) REVERT: C 95 MET cc_start: 0.8903 (tmm) cc_final: 0.8160 (tmm) REVERT: C 96 MET cc_start: 0.8336 (mmm) cc_final: 0.7709 (mmm) REVERT: C 109 PHE cc_start: 0.8355 (m-10) cc_final: 0.8091 (m-80) REVERT: C 124 TRP cc_start: 0.8043 (t60) cc_final: 0.7321 (t60) REVERT: C 162 TYR cc_start: 0.8787 (m-10) cc_final: 0.8100 (m-10) REVERT: C 271 LEU cc_start: 0.8457 (mt) cc_final: 0.8254 (mt) REVERT: D 20 MET cc_start: 0.9469 (mmm) cc_final: 0.9085 (ptm) REVERT: D 56 MET cc_start: 0.9165 (mmp) cc_final: 0.8561 (ptp) REVERT: D 79 GLU cc_start: 0.8361 (tm-30) cc_final: 0.6884 (tp30) REVERT: D 213 TYR cc_start: 0.6771 (t80) cc_final: 0.6432 (t80) REVERT: D 227 PHE cc_start: 0.8068 (m-10) cc_final: 0.7664 (m-80) REVERT: D 261 ARG cc_start: 0.7555 (ttm170) cc_final: 0.6683 (ptm160) outliers start: 55 outliers final: 25 residues processed: 570 average time/residue: 0.1048 time to fit residues: 90.1751 Evaluate side-chains 523 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 496 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.090147 restraints weight = 32529.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093313 restraints weight = 15255.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095332 restraints weight = 9061.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096624 restraints weight = 6338.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097483 restraints weight = 4958.467| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 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 = 0.3063 r_free = 0.3063 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: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16299 Z= 0.190 Angle : 0.671 15.309 22004 Z= 0.345 Chirality : 0.044 0.186 2348 Planarity : 0.004 0.044 2812 Dihedral : 6.690 62.650 2265 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.38 % Allowed : 22.99 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1928 helix: 1.09 (0.15), residues: 1140 sheet: 0.22 (0.43), residues: 126 loop : 0.44 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.039 0.002 TYR D 142 PHE 0.029 0.002 PHE D 168 TRP 0.022 0.002 TRP C 30 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (16298) covalent geometry : angle 0.67083 / 0.34 (22004) hydrogen bonds : bond 0.03963 / 2.53 ( 896) hydrogen bonds : angle 5.06131 / 3.56 ( 2616) Misc. bond : bond 0.00040 / 0.02 ( 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 560 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 502 time to evaluate : 0.609 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 11 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: A 119 GLU cc_start: 0.8499 (mp0) cc_final: 0.7993 (mp0) REVERT: A 135 GLU cc_start: 0.8608 (mp0) cc_final: 0.8403 (mp0) REVERT: A 139 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 147 GLN cc_start: 0.9330 (mt0) cc_final: 0.9094 (mt0) REVERT: A 174 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 178 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8272 (t) REVERT: A 214 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8278 (mmtm) REVERT: A 232 ASN cc_start: 0.9041 (m-40) cc_final: 0.8405 (m110) REVERT: A 256 ARG cc_start: 0.8937 (tpt90) cc_final: 0.8299 (tpt90) REVERT: A 334 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8369 (ptpt) REVERT: A 348 MET cc_start: 0.8868 (ttp) cc_final: 0.8591 (tmm) REVERT: A 362 ASP cc_start: 0.8495 (m-30) cc_final: 0.7941 (m-30) REVERT: A 393 SER cc_start: 0.8805 (m) cc_final: 0.8327 (p) REVERT: A 415 ASN cc_start: 0.8967 (t0) cc_final: 0.8750 (t0) REVERT: A 446 ARG cc_start: 0.7855 (mmp80) cc_final: 0.7437 (mmp80) REVERT: A 598 MET cc_start: 0.8212 (mtp) cc_final: 0.7878 (mtp) REVERT: A 599 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: A 602 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 604 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8257 (mmp80) REVERT: A 612 TYR cc_start: 0.8910 (m-80) cc_final: 0.8635 (m-80) REVERT: B 78 LYS cc_start: 0.9222 (pttm) cc_final: 0.8926 (pttp) REVERT: B 102 ASN cc_start: 0.9242 (m-40) cc_final: 0.8881 (m110) REVERT: B 104 TYR cc_start: 0.8998 (m-80) cc_final: 0.8640 (m-80) REVERT: B 172 LEU cc_start: 0.8994 (mp) cc_final: 0.8463 (mp) REVERT: B 181 ASP cc_start: 0.8647 (m-30) cc_final: 0.8261 (m-30) REVERT: B 184 ARG cc_start: 0.9120 (tpp-160) cc_final: 0.8842 (tpp80) REVERT: B 238 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7169 (t70) REVERT: B 515 ASP cc_start: 0.9091 (m-30) cc_final: 0.8814 (m-30) REVERT: B 639 ASP cc_start: 0.8501 (m-30) cc_final: 0.8081 (m-30) REVERT: B 686 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7786 (mpt180) REVERT: C 109 PHE cc_start: 0.8356 (m-10) cc_final: 0.8087 (m-80) REVERT: C 122 PHE cc_start: 0.9323 (t80) cc_final: 0.9096 (t80) REVERT: C 162 TYR cc_start: 0.8725 (m-10) cc_final: 0.8128 (m-10) REVERT: C 226 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8726 (pp20) REVERT: C 261 ARG cc_start: 0.5912 (mtp-110) cc_final: 0.5474 (mtm110) REVERT: C 271 LEU cc_start: 0.8585 (mt) cc_final: 0.8300 (mt) REVERT: D 20 MET cc_start: 0.9494 (mmm) cc_final: 0.9149 (ptm) REVERT: D 25 ASN cc_start: 0.9476 (m-40) cc_final: 0.9235 (m110) REVERT: D 56 MET cc_start: 0.9262 (mmp) cc_final: 0.8496 (ptp) REVERT: D 93 MET cc_start: 0.5873 (ppp) cc_final: 0.5537 (ptt) REVERT: D 109 PHE cc_start: 0.8238 (m-80) cc_final: 0.7779 (m-80) REVERT: D 227 PHE cc_start: 0.8222 (m-10) cc_final: 0.7776 (m-80) REVERT: D 261 ARG cc_start: 0.7500 (ttm170) cc_final: 0.6621 (ptm160) REVERT: D 273 PHE cc_start: 0.6602 (m-80) cc_final: 0.6088 (m-10) outliers start: 58 outliers final: 44 residues processed: 532 average time/residue: 0.1078 time to fit residues: 86.6068 Evaluate side-chains 529 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 479 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 474 GLN C 127 GLN C 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.090243 restraints weight = 32308.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093336 restraints weight = 15143.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.095311 restraints weight = 8986.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096655 restraints weight = 6321.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097548 restraints weight = 4936.440| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 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 = 0.3067 r_free = 0.3067 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: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16299 Z= 0.186 Angle : 0.673 12.784 22004 Z= 0.346 Chirality : 0.044 0.191 2348 Planarity : 0.004 0.047 2812 Dihedral : 6.711 63.562 2264 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.62 % Allowed : 23.28 % Favored : 73.10 % 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: 1.05 (0.19), residues: 1928 helix: 1.06 (0.15), residues: 1141 sheet: 0.21 (0.44), residues: 126 loop : 0.39 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.040 0.002 TYR D 142 PHE 0.037 0.002 PHE D 172 TRP 0.036 0.003 TRP C 30 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (16298) covalent geometry : angle 0.67337 / 0.35 (22004) hydrogen bonds : bond 0.03956 / 2.53 ( 896) hydrogen bonds : angle 5.06187 / 3.56 ( 2616) Misc. bond : bond 0.00037 / 0.02 ( 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 560 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 498 time to evaluate : 0.504 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 11 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8402 (mt0) REVERT: A 119 GLU cc_start: 0.8489 (mp0) cc_final: 0.8002 (mp0) REVERT: A 139 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8389 (mm-30) REVERT: A 164 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.6798 (ptm-80) REVERT: A 174 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 214 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8239 (mmtm) REVERT: A 232 ASN cc_start: 0.9053 (m-40) cc_final: 0.8848 (m110) REVERT: A 256 ARG cc_start: 0.8955 (tpt90) cc_final: 0.8395 (tpt90) REVERT: A 317 MET cc_start: 0.8363 (mtt) cc_final: 0.8112 (mtt) REVERT: A 334 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8392 (ptpt) REVERT: A 348 MET cc_start: 0.8869 (ttp) cc_final: 0.8565 (tmm) REVERT: A 362 ASP cc_start: 0.8511 (m-30) cc_final: 0.8125 (m-30) REVERT: A 393 SER cc_start: 0.8752 (m) cc_final: 0.8520 (p) REVERT: A 415 ASN cc_start: 0.8979 (t0) cc_final: 0.8778 (t0) REVERT: A 446 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7475 (mmp-170) REVERT: A 483 GLU cc_start: 0.8924 (mp0) cc_final: 0.8464 (pm20) REVERT: A 598 MET cc_start: 0.8247 (mtp) cc_final: 0.7920 (mtp) REVERT: A 599 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: A 602 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: A 604 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8226 (mmp80) REVERT: A 612 TYR cc_start: 0.8943 (m-80) cc_final: 0.8618 (m-80) REVERT: B 78 LYS cc_start: 0.9217 (pttm) cc_final: 0.8921 (pttp) REVERT: B 102 ASN cc_start: 0.9249 (m-40) cc_final: 0.8885 (m110) REVERT: B 104 TYR cc_start: 0.8988 (m-80) cc_final: 0.8656 (m-80) REVERT: B 172 LEU cc_start: 0.8882 (mp) cc_final: 0.8626 (mp) REVERT: B 181 ASP cc_start: 0.8662 (m-30) cc_final: 0.8268 (m-30) REVERT: B 184 ARG cc_start: 0.9138 (tpp-160) cc_final: 0.8881 (tpp80) REVERT: B 235 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8273 (ttm110) REVERT: B 238 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7165 (t70) REVERT: B 515 ASP cc_start: 0.9092 (m-30) cc_final: 0.8796 (m-30) REVERT: B 586 TYR cc_start: 0.9164 (m-80) cc_final: 0.8559 (m-80) REVERT: B 599 GLU cc_start: 0.8462 (pm20) cc_final: 0.8199 (pm20) REVERT: B 639 ASP cc_start: 0.8517 (m-30) cc_final: 0.8090 (m-30) REVERT: B 686 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7672 (mpt180) REVERT: C 17 PHE cc_start: 0.7695 (p90) cc_final: 0.6495 (p90) REVERT: C 74 MET cc_start: 0.6780 (mtt) cc_final: 0.6278 (mtm) REVERT: C 109 PHE cc_start: 0.8370 (m-10) cc_final: 0.8097 (m-80) REVERT: C 162 TYR cc_start: 0.8776 (m-10) cc_final: 0.8187 (m-10) REVERT: C 226 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8693 (pp20) REVERT: C 271 LEU cc_start: 0.8583 (mt) cc_final: 0.8310 (mt) REVERT: D 20 MET cc_start: 0.9496 (mmm) cc_final: 0.9159 (ptm) REVERT: D 25 ASN cc_start: 0.9467 (m-40) cc_final: 0.9206 (m110) REVERT: D 56 MET cc_start: 0.9244 (mmp) cc_final: 0.8494 (ptp) REVERT: D 109 PHE cc_start: 0.8393 (m-80) cc_final: 0.7900 (m-80) REVERT: D 134 LYS cc_start: 0.8118 (pttt) cc_final: 0.7237 (pttp) REVERT: D 157 MET cc_start: 0.6872 (ppp) cc_final: 0.6404 (ppp) REVERT: D 227 PHE cc_start: 0.8352 (m-10) cc_final: 0.7938 (m-80) REVERT: D 239 GLU cc_start: 0.7095 (pp20) cc_final: 0.6868 (pp20) REVERT: D 261 ARG cc_start: 0.7618 (ttm170) cc_final: 0.6594 (ptm160) REVERT: D 273 PHE cc_start: 0.6590 (m-80) cc_final: 0.6064 (m-10) outliers start: 62 outliers final: 43 residues processed: 534 average time/residue: 0.1090 time to fit residues: 87.6453 Evaluate side-chains 524 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 476 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 122 optimal weight: 0.0370 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095325 restraints weight = 32696.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098530 restraints weight = 15062.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100596 restraints weight = 8888.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101888 restraints weight = 6150.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102854 restraints weight = 4812.419| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 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 = 0.3123 r_free = 0.3123 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: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16299 Z= 0.133 Angle : 0.672 12.394 22004 Z= 0.345 Chirality : 0.044 0.236 2348 Planarity : 0.003 0.048 2812 Dihedral : 6.546 61.658 2264 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.04 % Allowed : 25.61 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1928 helix: 1.05 (0.15), residues: 1145 sheet: 0.19 (0.44), residues: 126 loop : 0.33 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.041 0.001 TYR D 142 PHE 0.024 0.001 PHE D 259 TRP 0.034 0.002 TRP C 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16298) covalent geometry : angle 0.67242 / 0.34 (22004) hydrogen bonds : bond 0.03867 / 2.49 ( 896) hydrogen bonds : angle 5.01930 / 3.52 ( 2616) Misc. bond : bond 0.00033 / 0.02 ( 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 547 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 512 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: A 95 MET cc_start: 0.9029 (tpp) cc_final: 0.8826 (tpp) REVERT: A 106 LEU cc_start: 0.9412 (tp) cc_final: 0.9141 (tp) REVERT: A 115 LEU cc_start: 0.8937 (mp) cc_final: 0.8400 (mt) REVERT: A 119 GLU cc_start: 0.8451 (mp0) cc_final: 0.7973 (mp0) REVERT: A 139 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8407 (mm-30) REVERT: A 174 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 191 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 214 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8065 (mmtm) REVERT: A 232 ASN cc_start: 0.9039 (m-40) cc_final: 0.8432 (m110) REVERT: A 256 ARG cc_start: 0.8917 (tpt90) cc_final: 0.8204 (tpt90) REVERT: A 334 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8254 (ptpt) REVERT: A 348 MET cc_start: 0.8871 (ttp) cc_final: 0.8575 (tmm) REVERT: A 446 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7531 (mmp-170) REVERT: A 483 GLU cc_start: 0.8877 (mp0) cc_final: 0.8443 (pm20) REVERT: A 493 MET cc_start: 0.8814 (tmm) cc_final: 0.8610 (tmm) REVERT: A 599 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: A 602 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: A 604 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8215 (mmp80) REVERT: A 612 TYR cc_start: 0.8827 (m-80) cc_final: 0.8450 (m-80) REVERT: A 657 PHE cc_start: 0.9045 (m-80) cc_final: 0.8809 (m-80) REVERT: A 686 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7235 (mtp85) REVERT: B 37 PHE cc_start: 0.8878 (m-10) cc_final: 0.8623 (m-10) REVERT: B 78 LYS cc_start: 0.9214 (pttm) cc_final: 0.8939 (pttp) REVERT: B 102 ASN cc_start: 0.9167 (m-40) cc_final: 0.8815 (m110) REVERT: B 104 TYR cc_start: 0.8919 (m-80) cc_final: 0.8605 (m-80) REVERT: B 161 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7851 (mtt180) REVERT: B 172 LEU cc_start: 0.8861 (mp) cc_final: 0.8562 (mp) REVERT: B 181 ASP cc_start: 0.8609 (m-30) cc_final: 0.8171 (m-30) REVERT: B 184 ARG cc_start: 0.9128 (tpp-160) cc_final: 0.8732 (tpp80) REVERT: B 235 ARG cc_start: 0.8833 (ttp-110) cc_final: 0.8358 (ttm110) REVERT: B 238 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7135 (t70) REVERT: B 250 TYR cc_start: 0.9176 (m-80) cc_final: 0.8874 (m-80) REVERT: B 463 LEU cc_start: 0.9168 (tp) cc_final: 0.8910 (tp) REVERT: B 515 ASP cc_start: 0.9034 (m-30) cc_final: 0.8804 (m-30) REVERT: B 586 TYR cc_start: 0.9083 (m-80) cc_final: 0.8679 (m-80) REVERT: B 639 ASP cc_start: 0.8562 (m-30) cc_final: 0.8084 (m-30) REVERT: B 686 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7672 (mpt180) REVERT: C 74 MET cc_start: 0.6925 (mtt) cc_final: 0.6267 (mtm) REVERT: C 103 LYS cc_start: 0.5235 (mmtt) cc_final: 0.5004 (mptt) REVERT: C 109 PHE cc_start: 0.8352 (m-10) cc_final: 0.8111 (m-80) REVERT: C 158 VAL cc_start: 0.9630 (t) cc_final: 0.8874 (m) REVERT: C 162 TYR cc_start: 0.8719 (m-10) cc_final: 0.8213 (m-10) REVERT: C 226 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8671 (pp20) REVERT: D 20 MET cc_start: 0.9471 (mmm) cc_final: 0.9206 (ptm) REVERT: D 25 ASN cc_start: 0.9506 (m-40) cc_final: 0.9225 (m110) REVERT: D 56 MET cc_start: 0.9195 (mmp) cc_final: 0.8455 (ptp) REVERT: D 109 PHE cc_start: 0.8349 (m-80) cc_final: 0.7896 (m-80) REVERT: D 134 LYS cc_start: 0.8062 (pttt) cc_final: 0.7241 (pttp) REVERT: D 157 MET cc_start: 0.6825 (ppp) cc_final: 0.6340 (ppp) REVERT: D 227 PHE cc_start: 0.8401 (m-10) cc_final: 0.8009 (m-80) REVERT: D 261 ARG cc_start: 0.7344 (ttm170) cc_final: 0.6652 (ptm160) outliers start: 35 outliers final: 24 residues processed: 532 average time/residue: 0.1073 time to fit residues: 86.1692 Evaluate side-chains 510 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 481 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 246 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: 4.9990 chunk 143 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.090465 restraints weight = 32529.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.093670 restraints weight = 15331.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095701 restraints weight = 9059.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097002 restraints weight = 6308.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097818 restraints weight = 4943.022| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16299 Z= 0.196 Angle : 0.713 15.061 22004 Z= 0.366 Chirality : 0.045 0.281 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.674 63.149 2264 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 26.14 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 1928 helix: 1.03 (0.15), residues: 1131 sheet: 0.06 (0.44), residues: 126 loop : 0.40 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.041 0.002 TYR D 142 PHE 0.026 0.002 PHE D 172 TRP 0.036 0.003 TRP C 30 HIS 0.016 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (16298) covalent geometry : angle 0.71287 / 0.37 (22004) hydrogen bonds : bond 0.03960 / 2.55 ( 896) hydrogen bonds : angle 5.15107 / 3.62 ( 2616) Misc. bond : bond 0.00032 / 0.02 ( 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 527 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 491 time to evaluate : 0.401 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 11 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8402 (mt0) REVERT: A 119 GLU cc_start: 0.8458 (mp0) cc_final: 0.7971 (mp0) REVERT: A 174 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 191 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7939 (mm-40) REVERT: A 214 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8174 (mmtm) REVERT: A 256 ARG cc_start: 0.8956 (tpt90) cc_final: 0.8249 (tpt90) REVERT: A 317 MET cc_start: 0.8311 (mtt) cc_final: 0.7964 (mtt) REVERT: A 334 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8363 (ptpt) REVERT: A 348 MET cc_start: 0.8908 (ttp) cc_final: 0.8608 (tmm) REVERT: A 446 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7645 (mmp80) REVERT: A 453 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8913 (ttt-90) REVERT: A 483 GLU cc_start: 0.8942 (mp0) cc_final: 0.8461 (pm20) REVERT: A 604 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8311 (mmp80) REVERT: A 612 TYR cc_start: 0.8895 (m-80) cc_final: 0.8437 (m-80) REVERT: A 637 VAL cc_start: 0.9450 (t) cc_final: 0.9185 (p) REVERT: A 686 ARG cc_start: 0.7528 (mtp85) cc_final: 0.7130 (mtp85) REVERT: B 78 LYS cc_start: 0.9216 (pttm) cc_final: 0.8880 (pttp) REVERT: B 102 ASN cc_start: 0.9165 (m-40) cc_final: 0.8817 (m110) REVERT: B 104 TYR cc_start: 0.9110 (m-80) cc_final: 0.8703 (m-80) REVERT: B 129 PHE cc_start: 0.9546 (m-10) cc_final: 0.9337 (m-10) REVERT: B 147 GLN cc_start: 0.9398 (mm110) cc_final: 0.9039 (mm110) REVERT: B 161 ARG cc_start: 0.8250 (mtt180) cc_final: 0.8016 (mtt180) REVERT: B 172 LEU cc_start: 0.8904 (mp) cc_final: 0.8649 (mp) REVERT: B 181 ASP cc_start: 0.8611 (m-30) cc_final: 0.8229 (m-30) REVERT: B 184 ARG cc_start: 0.9094 (tpp-160) cc_final: 0.8870 (tpp80) REVERT: B 235 ARG cc_start: 0.8876 (ttp-110) cc_final: 0.8310 (ttm110) REVERT: B 238 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7079 (t70) REVERT: B 250 TYR cc_start: 0.9217 (m-80) cc_final: 0.8907 (m-80) REVERT: B 463 LEU cc_start: 0.9205 (tp) cc_final: 0.8954 (tp) REVERT: B 515 ASP cc_start: 0.9101 (m-30) cc_final: 0.8780 (m-30) REVERT: B 586 TYR cc_start: 0.9146 (m-80) cc_final: 0.8835 (m-80) REVERT: B 639 ASP cc_start: 0.8519 (m-30) cc_final: 0.8071 (m-30) REVERT: B 686 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7651 (mpt180) REVERT: C 74 MET cc_start: 0.6923 (mtt) cc_final: 0.6340 (mtm) REVERT: C 109 PHE cc_start: 0.8294 (m-10) cc_final: 0.7565 (m-80) REVERT: C 145 ILE cc_start: 0.8542 (mt) cc_final: 0.8331 (tp) REVERT: C 158 VAL cc_start: 0.9545 (t) cc_final: 0.8890 (m) REVERT: C 162 TYR cc_start: 0.8812 (m-10) cc_final: 0.8315 (m-10) REVERT: C 226 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8647 (pp20) REVERT: C 237 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9160 (pp20) REVERT: D 20 MET cc_start: 0.9495 (mmm) cc_final: 0.9219 (ptm) REVERT: D 25 ASN cc_start: 0.9466 (m-40) cc_final: 0.9178 (m110) REVERT: D 56 MET cc_start: 0.9211 (mmp) cc_final: 0.8449 (ptp) REVERT: D 109 PHE cc_start: 0.8400 (m-80) cc_final: 0.7937 (m-80) REVERT: D 134 LYS cc_start: 0.8058 (pttt) cc_final: 0.7263 (pttp) REVERT: D 157 MET cc_start: 0.6920 (ppp) cc_final: 0.6531 (ppp) REVERT: D 227 PHE cc_start: 0.8448 (m-10) cc_final: 0.8085 (m-80) outliers start: 36 outliers final: 28 residues processed: 510 average time/residue: 0.1086 time to fit residues: 83.1179 Evaluate side-chains 504 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 472 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.091652 restraints weight = 32959.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094752 restraints weight = 15245.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096736 restraints weight = 9032.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.098086 restraints weight = 6345.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098967 restraints weight = 4935.458| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 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 = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16299 Z= 0.227 Angle : 0.739 14.938 22004 Z= 0.383 Chirality : 0.047 0.304 2348 Planarity : 0.004 0.047 2812 Dihedral : 6.863 63.435 2264 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.10 % Allowed : 26.20 % Favored : 71.70 % 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: 0.82 (0.19), residues: 1928 helix: 0.91 (0.15), residues: 1132 sheet: -0.60 (0.42), residues: 148 loop : 0.44 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.041 0.002 TYR C 105 PHE 0.030 0.002 PHE D 172 TRP 0.031 0.003 TRP C 30 HIS 0.013 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (16298) covalent geometry : angle 0.73857 / 0.38 (22004) hydrogen bonds : bond 0.04142 / 2.64 ( 896) hydrogen bonds : angle 5.25465 / 3.70 ( 2616) Misc. bond : bond 0.00037 / 0.02 ( 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 514 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 478 time to evaluate : 0.596 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 11 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8419 (mt0) REVERT: A 65 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8104 (mp0) REVERT: A 214 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8216 (mmtm) REVERT: A 256 ARG cc_start: 0.9006 (tpt90) cc_final: 0.8425 (tpt90) REVERT: A 317 MET cc_start: 0.8369 (mtt) cc_final: 0.8022 (mtt) REVERT: A 334 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8400 (ptpt) REVERT: A 446 ARG cc_start: 0.8127 (mmp80) cc_final: 0.7784 (mmp80) REVERT: A 453 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8888 (ttt-90) REVERT: A 483 GLU cc_start: 0.8938 (mp0) cc_final: 0.8443 (pm20) REVERT: A 612 TYR cc_start: 0.8922 (m-80) cc_final: 0.8473 (m-80) REVERT: A 686 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7171 (mtp85) REVERT: B 78 LYS cc_start: 0.9216 (pttm) cc_final: 0.8891 (pttp) REVERT: B 102 ASN cc_start: 0.9183 (m-40) cc_final: 0.8832 (m110) REVERT: B 104 TYR cc_start: 0.9150 (m-80) cc_final: 0.8760 (m-80) REVERT: B 148 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8465 (mt-10) REVERT: B 161 ARG cc_start: 0.8294 (mtt180) cc_final: 0.8027 (mtt180) REVERT: B 181 ASP cc_start: 0.8655 (m-30) cc_final: 0.8276 (m-30) REVERT: B 184 ARG cc_start: 0.9098 (tpp-160) cc_final: 0.8875 (tpp80) REVERT: B 238 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7172 (t70) REVERT: B 515 ASP cc_start: 0.9119 (m-30) cc_final: 0.8795 (m-30) REVERT: B 586 TYR cc_start: 0.9175 (m-80) cc_final: 0.8855 (m-80) REVERT: B 639 ASP cc_start: 0.8529 (m-30) cc_final: 0.8070 (m-30) REVERT: B 686 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7615 (mpt180) REVERT: C 74 MET cc_start: 0.7124 (mtt) cc_final: 0.6514 (mtm) REVERT: C 105 TYR cc_start: 0.6241 (p90) cc_final: 0.5806 (p90) REVERT: C 162 TYR cc_start: 0.8864 (m-10) cc_final: 0.8292 (m-10) REVERT: C 226 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8610 (pp20) REVERT: D 20 MET cc_start: 0.9450 (mmm) cc_final: 0.9222 (ptm) REVERT: D 25 ASN cc_start: 0.9480 (m-40) cc_final: 0.9183 (m110) REVERT: D 134 LYS cc_start: 0.7988 (pttt) cc_final: 0.7762 (pttp) REVERT: D 157 MET cc_start: 0.7014 (ppp) cc_final: 0.6640 (ppp) REVERT: D 189 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8037 (tm-30) REVERT: D 227 PHE cc_start: 0.8473 (m-10) cc_final: 0.8145 (m-80) REVERT: D 261 ARG cc_start: 0.7442 (ttm170) cc_final: 0.6832 (ptm160) outliers start: 36 outliers final: 29 residues processed: 497 average time/residue: 0.1117 time to fit residues: 83.3434 Evaluate side-chains 492 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 459 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 40.0000 chunk 146 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 588 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.094323 restraints weight = 32657.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097560 restraints weight = 15020.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099706 restraints weight = 8815.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100971 restraints weight = 6086.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101922 restraints weight = 4761.174| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16299 Z= 0.155 Angle : 0.746 16.818 22004 Z= 0.380 Chirality : 0.046 0.275 2348 Planarity : 0.004 0.046 2812 Dihedral : 6.730 62.546 2264 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.81 % Allowed : 26.90 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1928 helix: 0.82 (0.15), residues: 1145 sheet: -0.05 (0.45), residues: 128 loop : 0.24 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.042 0.002 TYR D 142 PHE 0.044 0.002 PHE D 122 TRP 0.035 0.002 TRP C 30 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16298) covalent geometry : angle 0.74595 / 0.38 (22004) hydrogen bonds : bond 0.04082 / 2.61 ( 896) hydrogen bonds : angle 5.22193 / 3.70 ( 2616) Misc. bond : bond 0.00031 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.82 seconds wall clock time: 51 minutes 8.73 seconds (3068.73 seconds total)