Starting phenix.real_space_refine on Fri Jul 3 19:27:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx3_44992/07_2026/9bx3_44992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx3_44992/07_2026/9bx3_44992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx3_44992/07_2026/9bx3_44992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx3_44992/07_2026/9bx3_44992.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx3_44992/07_2026/9bx3_44992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx3_44992/07_2026/9bx3_44992_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.88, per 1000 atoms: 0.24 Number of scatterers: 15954 At special positions: 0 Unit cell: (91.98, 126.728, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 683.4 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: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.553A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.705A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.872A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.792A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.273A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.950A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.961A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.778A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.574A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.175A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.737A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4974 1.34 - 1.46: 2945 1.46 - 1.58: 8204 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.607 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.30e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 21467 2.11 - 4.23: 464 4.23 - 6.34: 58 6.34 - 8.45: 8 8.45 - 10.57: 7 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.66 10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 8642 17.65 - 35.29: 855 35.29 - 52.94: 255 52.94 - 70.59: 64 70.59 - 88.24: 40 Dihedral angle restraints: 9856 sinusoidal: 4110 harmonic: 5746 Sorted by residual: dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" N VAL C 125 " pdb=" C VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual 123.40 135.55 -12.15 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" C ASN C 98 " pdb=" N ASN C 98 " pdb=" CA ASN C 98 " pdb=" CB ASN C 98 " ideal model delta harmonic sigma weight residual -122.60 -134.35 11.75 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2122 0.093 - 0.187: 187 0.187 - 0.280: 33 0.280 - 0.374: 4 0.374 - 0.467: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11873 3.11 - 3.70: 26426 3.70 - 4.30: 41198 4.30 - 4.90: 64928 Nonbonded interactions: 144556 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 ... (remaining 144551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.860 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.834 16299 Z= 0.732 Angle : 0.756 10.566 22004 Z= 0.461 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.910 88.236 6168 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.33 (16298) covalent geometry : angle 0.75600 / 0.46 (22004) hydrogen bonds : bond 0.16171 / 10.53 ( 896) hydrogen bonds : angle 6.35194 / 4.48 ( 2616) Misc. bond : bond 0.83355 / 43.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7477 (p0) cc_final: 0.7151 (p0) REVERT: A 35 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 200 SER cc_start: 0.8921 (t) cc_final: 0.8679 (t) REVERT: A 204 SER cc_start: 0.8532 (m) cc_final: 0.8297 (p) REVERT: A 349 LEU cc_start: 0.8108 (tp) cc_final: 0.7850 (tp) REVERT: A 359 MET cc_start: 0.7680 (ttt) cc_final: 0.7411 (ttt) REVERT: A 411 LEU cc_start: 0.8571 (mt) cc_final: 0.8292 (mt) REVERT: A 658 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 27 ASP cc_start: 0.7317 (p0) cc_final: 0.7082 (p0) REVERT: B 72 TYR cc_start: 0.7028 (m-80) cc_final: 0.6372 (m-10) REVERT: B 100 PHE cc_start: 0.8143 (t80) cc_final: 0.7863 (t80) REVERT: B 187 ASP cc_start: 0.7691 (t70) cc_final: 0.7430 (t0) REVERT: B 200 SER cc_start: 0.8916 (t) cc_final: 0.8319 (t) REVERT: B 211 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 235 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7601 (ttm-80) REVERT: B 246 SER cc_start: 0.8358 (m) cc_final: 0.7988 (p) REVERT: B 250 TYR cc_start: 0.8608 (m-80) cc_final: 0.8175 (m-80) REVERT: B 288 PHE cc_start: 0.8346 (t80) cc_final: 0.7903 (t80) REVERT: B 373 ILE cc_start: 0.8752 (mt) cc_final: 0.8165 (mt) REVERT: B 379 SER cc_start: 0.8708 (t) cc_final: 0.8091 (t) REVERT: B 415 ASN cc_start: 0.7985 (t0) cc_final: 0.7739 (t0) REVERT: B 420 MET cc_start: 0.8428 (mmm) cc_final: 0.8163 (mmm) REVERT: B 425 ILE cc_start: 0.9006 (mt) cc_final: 0.8711 (mt) REVERT: B 490 THR cc_start: 0.8636 (m) cc_final: 0.8411 (m) REVERT: B 494 MET cc_start: 0.7414 (mtp) cc_final: 0.7107 (mtp) REVERT: B 550 MET cc_start: 0.7872 (ttm) cc_final: 0.7311 (ttm) REVERT: B 558 TRP cc_start: 0.8481 (m100) cc_final: 0.8031 (m100) REVERT: B 626 TYR cc_start: 0.8053 (m-80) cc_final: 0.7768 (m-80) REVERT: C 157 MET cc_start: 0.7101 (mtt) cc_final: 0.6738 (mtp) REVERT: C 224 LEU cc_start: 0.4867 (mt) cc_final: 0.4572 (mt) REVERT: C 260 ILE cc_start: 0.6261 (pt) cc_final: 0.5525 (pt) REVERT: D 47 LEU cc_start: 0.4053 (mt) cc_final: 0.3757 (mp) REVERT: D 56 MET cc_start: 0.5125 (mmp) cc_final: 0.4713 (mtt) REVERT: D 67 THR cc_start: 0.7180 (m) cc_final: 0.6843 (m) REVERT: D 321 TYR cc_start: 0.6611 (m-80) cc_final: 0.6092 (t80) outliers start: 23 outliers final: 4 residues processed: 875 average time/residue: 0.1421 time to fit residues: 181.1154 Evaluate side-chains 606 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 600 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 14 ASN B 158 ASN B 645 GLN C 23 ASN C 25 ASN C 28 GLN C 52 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 186 GLN D 201 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095422 restraints weight = 34046.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099069 restraints weight = 16981.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101374 restraints weight = 10216.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102494 restraints weight = 7208.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103665 restraints weight = 5847.950| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16299 Z= 0.195 Angle : 0.683 10.487 22004 Z= 0.364 Chirality : 0.044 0.182 2348 Planarity : 0.004 0.054 2812 Dihedral : 7.113 59.235 2273 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.21 % Allowed : 19.66 % Favored : 77.13 % 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: 1.48 (0.18), residues: 1928 helix: 1.37 (0.15), residues: 1124 sheet: 1.24 (0.43), residues: 98 loop : 0.49 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.027 0.002 TYR C 142 PHE 0.038 0.002 PHE C 168 TRP 0.020 0.002 TRP C 44 HIS 0.011 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (16298) covalent geometry : angle 0.68265 / 0.36 (22004) hydrogen bonds : bond 0.04880 / 3.10 ( 896) hydrogen bonds : angle 5.31184 / 3.70 ( 2616) Misc. bond : bond 0.00125 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 653 time to evaluate : 0.634 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 172 LEU cc_start: 0.9228 (mp) cc_final: 0.8444 (mp) REVERT: A 179 LEU cc_start: 0.9383 (tp) cc_final: 0.9125 (tp) REVERT: A 204 SER cc_start: 0.9039 (m) cc_final: 0.8831 (p) REVERT: A 218 ASN cc_start: 0.8460 (t0) cc_final: 0.8187 (t0) REVERT: A 315 ASP cc_start: 0.8028 (p0) cc_final: 0.7734 (p0) REVERT: A 316 GLU cc_start: 0.8140 (tt0) cc_final: 0.7667 (tm-30) REVERT: A 355 TYR cc_start: 0.8286 (m-80) cc_final: 0.8069 (m-10) REVERT: A 383 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8431 (t) REVERT: A 406 ASP cc_start: 0.7995 (m-30) cc_final: 0.7315 (t0) REVERT: A 485 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7697 (mtt90) REVERT: A 493 MET cc_start: 0.8916 (tmm) cc_final: 0.8622 (tmm) REVERT: A 526 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 550 MET cc_start: 0.7740 (mtp) cc_final: 0.7327 (mtm) REVERT: A 646 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: A 657 PHE cc_start: 0.8683 (m-80) cc_final: 0.8402 (m-80) REVERT: A 662 MET cc_start: 0.8404 (mmp) cc_final: 0.8072 (mmp) REVERT: B 27 ASP cc_start: 0.8684 (p0) cc_final: 0.8414 (p0) REVERT: B 31 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: B 109 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8720 (m110) REVERT: B 161 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7588 (mtt180) REVERT: B 200 SER cc_start: 0.8949 (t) cc_final: 0.8243 (t) REVERT: B 232 ASN cc_start: 0.8967 (t0) cc_final: 0.8470 (m-40) REVERT: B 246 SER cc_start: 0.7726 (m) cc_final: 0.7330 (p) REVERT: B 250 TYR cc_start: 0.9262 (m-80) cc_final: 0.8072 (m-80) REVERT: B 288 PHE cc_start: 0.9287 (t80) cc_final: 0.8997 (t80) REVERT: B 322 MET cc_start: 0.9188 (mmm) cc_final: 0.8987 (mmp) REVERT: B 379 SER cc_start: 0.8828 (t) cc_final: 0.8023 (t) REVERT: B 381 LEU cc_start: 0.9268 (tp) cc_final: 0.9062 (tp) REVERT: B 467 ASN cc_start: 0.9145 (t0) cc_final: 0.8525 (m-40) REVERT: B 480 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 586 TYR cc_start: 0.8432 (m-80) cc_final: 0.7972 (m-80) REVERT: B 590 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8160 (t) REVERT: B 591 THR cc_start: 0.9126 (p) cc_final: 0.8827 (p) REVERT: B 599 GLU cc_start: 0.8089 (pt0) cc_final: 0.7861 (pt0) REVERT: B 601 ILE cc_start: 0.9134 (mm) cc_final: 0.8364 (mm) REVERT: B 602 GLU cc_start: 0.8134 (tt0) cc_final: 0.7420 (tt0) REVERT: B 604 ARG cc_start: 0.8947 (mmp80) cc_final: 0.8199 (tpp-160) REVERT: B 628 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 640 MET cc_start: 0.9090 (tpp) cc_final: 0.8611 (tpp) REVERT: B 667 LEU cc_start: 0.9045 (tt) cc_final: 0.8472 (tt) REVERT: C 64 LEU cc_start: 0.5564 (tp) cc_final: 0.4937 (pp) REVERT: C 117 THR cc_start: 0.7887 (p) cc_final: 0.7673 (t) REVERT: C 168 PHE cc_start: 0.7840 (m-80) cc_final: 0.7640 (m-80) REVERT: C 178 PHE cc_start: 0.8287 (m-80) cc_final: 0.7667 (m-10) REVERT: C 193 LEU cc_start: 0.8668 (mm) cc_final: 0.8120 (mt) REVERT: C 224 LEU cc_start: 0.7539 (mt) cc_final: 0.7222 (mt) REVERT: C 239 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8411 (pp20) REVERT: D 20 MET cc_start: 0.8821 (ptm) cc_final: 0.8589 (ppp) REVERT: D 24 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: D 56 MET cc_start: 0.3087 (mmp) cc_final: 0.2707 (mtt) REVERT: D 116 GLU cc_start: 0.8441 (pm20) cc_final: 0.8150 (pm20) REVERT: D 131 LEU cc_start: 0.8240 (tt) cc_final: 0.7385 (tt) REVERT: D 174 TYR cc_start: 0.4263 (t80) cc_final: 0.3629 (t80) REVERT: D 189 GLU cc_start: 0.8611 (tp30) cc_final: 0.8048 (mt-10) REVERT: D 204 TYR cc_start: 0.8811 (t80) cc_final: 0.8322 (t80) REVERT: D 216 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7576 (mm110) REVERT: D 277 PHE cc_start: 0.6235 (m-10) cc_final: 0.5906 (m-10) outliers start: 55 outliers final: 23 residues processed: 676 average time/residue: 0.1327 time to fit residues: 132.8713 Evaluate side-chains 600 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 570 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN A 668 ASN B 43 GLN B 232 ASN B 370 ASN ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 646 GLN C 23 ASN C 28 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091739 restraints weight = 35209.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095046 restraints weight = 17117.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097189 restraints weight = 10348.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098670 restraints weight = 7211.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099612 restraints weight = 5556.517| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4957 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= 0.233 Angle : 0.653 9.520 22004 Z= 0.351 Chirality : 0.044 0.171 2348 Planarity : 0.004 0.055 2812 Dihedral : 7.093 52.535 2267 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.91 % Allowed : 21.59 % Favored : 74.50 % 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: 1.34 (0.19), residues: 1928 helix: 1.35 (0.15), residues: 1129 sheet: -0.08 (0.39), residues: 142 loop : 0.51 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 196 TYR 0.021 0.002 TYR D 236 PHE 0.040 0.002 PHE D 172 TRP 0.015 0.002 TRP C 30 HIS 0.008 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (16298) covalent geometry : angle 0.65275 / 0.35 (22004) hydrogen bonds : bond 0.04467 / 2.83 ( 896) hydrogen bonds : angle 5.24719 / 3.65 ( 2616) Misc. bond : bond 0.00008 / 0.00 ( 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 662 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 595 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 172 LEU cc_start: 0.9300 (mp) cc_final: 0.9033 (mp) REVERT: A 218 ASN cc_start: 0.8667 (t0) cc_final: 0.8399 (t0) REVERT: A 312 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: A 317 MET cc_start: 0.9099 (mtm) cc_final: 0.8325 (mtt) REVERT: A 322 MET cc_start: 0.8386 (tpp) cc_final: 0.8018 (tpp) REVERT: A 355 TYR cc_start: 0.8284 (m-80) cc_final: 0.8048 (m-10) REVERT: A 383 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8669 (t) REVERT: A 485 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7671 (mtt90) REVERT: A 493 MET cc_start: 0.8857 (tmm) cc_final: 0.8425 (tmm) REVERT: B 31 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: B 167 LEU cc_start: 0.9013 (mt) cc_final: 0.8726 (mt) REVERT: B 200 SER cc_start: 0.8935 (t) cc_final: 0.8150 (t) REVERT: B 232 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8524 (m-40) REVERT: B 246 SER cc_start: 0.7903 (m) cc_final: 0.7286 (p) REVERT: B 250 TYR cc_start: 0.9274 (m-80) cc_final: 0.8108 (m-80) REVERT: B 286 ASP cc_start: 0.8202 (m-30) cc_final: 0.7806 (m-30) REVERT: B 288 PHE cc_start: 0.9278 (t80) cc_final: 0.9072 (t80) REVERT: B 322 MET cc_start: 0.9325 (mmm) cc_final: 0.9105 (mmt) REVERT: B 348 MET cc_start: 0.7494 (tpp) cc_final: 0.7283 (tpp) REVERT: B 379 SER cc_start: 0.8795 (t) cc_final: 0.8010 (t) REVERT: B 467 ASN cc_start: 0.9074 (t0) cc_final: 0.8872 (t0) REVERT: B 550 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: B 552 ILE cc_start: 0.9457 (mp) cc_final: 0.9214 (mt) REVERT: B 601 ILE cc_start: 0.9194 (mm) cc_final: 0.8143 (mm) REVERT: B 604 ARG cc_start: 0.8881 (mmp80) cc_final: 0.8233 (mmp80) REVERT: B 640 MET cc_start: 0.9081 (tpp) cc_final: 0.8615 (tpp) REVERT: B 670 ILE cc_start: 0.9297 (mm) cc_final: 0.9084 (mt) REVERT: C 56 MET cc_start: -0.4206 (tpt) cc_final: -0.4520 (tpp) REVERT: C 168 PHE cc_start: 0.7896 (m-80) cc_final: 0.7636 (m-80) REVERT: C 178 PHE cc_start: 0.8244 (m-80) cc_final: 0.7614 (m-10) REVERT: C 179 TYR cc_start: 0.8479 (t80) cc_final: 0.8159 (t80) REVERT: C 218 GLU cc_start: 0.9345 (mp0) cc_final: 0.8791 (pp20) REVERT: C 239 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8423 (pp20) REVERT: C 240 LEU cc_start: 0.8061 (mt) cc_final: 0.7768 (mp) REVERT: D 18 THR cc_start: 0.6483 (p) cc_final: 0.6183 (p) REVERT: D 101 HIS cc_start: 0.5281 (m-70) cc_final: 0.4875 (m170) REVERT: D 131 LEU cc_start: 0.8262 (tt) cc_final: 0.7933 (mt) REVERT: D 149 ASP cc_start: 0.7627 (t0) cc_final: 0.7359 (t70) REVERT: D 174 TYR cc_start: 0.4014 (t80) cc_final: 0.3235 (t80) REVERT: D 179 TYR cc_start: 0.8011 (t80) cc_final: 0.7437 (t80) REVERT: D 189 GLU cc_start: 0.8615 (tp30) cc_final: 0.7528 (mt-10) REVERT: D 204 TYR cc_start: 0.8753 (t80) cc_final: 0.8325 (t80) REVERT: D 216 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7554 (mm110) outliers start: 67 outliers final: 34 residues processed: 627 average time/residue: 0.1285 time to fit residues: 120.7889 Evaluate side-chains 569 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 530 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 646 GLN A 668 ASN B 62 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094728 restraints weight = 34637.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098114 restraints weight = 17405.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100239 restraints weight = 10643.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101613 restraints weight = 7573.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102501 restraints weight = 5962.435| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16299 Z= 0.144 Angle : 0.628 11.970 22004 Z= 0.332 Chirality : 0.043 0.200 2348 Planarity : 0.004 0.052 2812 Dihedral : 6.891 57.187 2265 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.86 % Allowed : 23.05 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1928 helix: 1.29 (0.15), residues: 1141 sheet: -0.15 (0.39), residues: 134 loop : 0.30 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.025 0.001 TYR C 22 PHE 0.030 0.002 PHE D 172 TRP 0.022 0.002 TRP C 30 HIS 0.004 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16298) covalent geometry : angle 0.62848 / 0.33 (22004) hydrogen bonds : bond 0.04152 / 2.61 ( 896) hydrogen bonds : angle 5.10307 / 3.54 ( 2616) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 588 time to evaluate : 0.529 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 166 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 218 ASN cc_start: 0.8644 (t0) cc_final: 0.8387 (t0) REVERT: A 322 MET cc_start: 0.8308 (tpp) cc_final: 0.7728 (tpp) REVERT: A 350 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7846 (mtp180) REVERT: A 383 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.8707 (t) REVERT: A 485 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7635 (mtt90) REVERT: A 493 MET cc_start: 0.8942 (tmm) cc_final: 0.8498 (tmm) REVERT: A 599 GLU cc_start: 0.8196 (mp0) cc_final: 0.7919 (mp0) REVERT: A 604 ARG cc_start: 0.8298 (tpp80) cc_final: 0.8044 (mmp80) REVERT: A 606 TYR cc_start: 0.8430 (m-80) cc_final: 0.8193 (m-80) REVERT: A 646 GLN cc_start: 0.9155 (mt0) cc_final: 0.8340 (mp10) REVERT: A 684 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: B 31 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: B 116 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8034 (mp0) REVERT: B 200 SER cc_start: 0.8911 (t) cc_final: 0.8023 (t) REVERT: B 228 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8403 (tppt) REVERT: B 232 ASN cc_start: 0.8992 (m-40) cc_final: 0.8552 (m-40) REVERT: B 246 SER cc_start: 0.7610 (m) cc_final: 0.7297 (p) REVERT: B 250 TYR cc_start: 0.9189 (m-80) cc_final: 0.8070 (m-80) REVERT: B 288 PHE cc_start: 0.9179 (t80) cc_final: 0.8920 (t80) REVERT: B 348 MET cc_start: 0.7492 (tpp) cc_final: 0.7232 (tpp) REVERT: B 379 SER cc_start: 0.8740 (t) cc_final: 0.7608 (t) REVERT: B 466 MET cc_start: 0.8919 (ptm) cc_final: 0.8612 (ptm) REVERT: B 494 MET cc_start: 0.8879 (mtp) cc_final: 0.8615 (mtp) REVERT: B 550 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7243 (ttm) REVERT: B 589 SER cc_start: 0.9528 (t) cc_final: 0.9120 (p) REVERT: B 601 ILE cc_start: 0.8961 (mm) cc_final: 0.8623 (mm) REVERT: B 639 ASP cc_start: 0.8534 (m-30) cc_final: 0.7999 (m-30) REVERT: B 640 MET cc_start: 0.9029 (tpp) cc_final: 0.8630 (tpp) REVERT: B 670 ILE cc_start: 0.9280 (mm) cc_final: 0.9077 (mt) REVERT: B 686 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7808 (mtm-85) REVERT: C 56 MET cc_start: -0.4887 (tpt) cc_final: -0.5126 (tpp) REVERT: C 168 PHE cc_start: 0.7858 (m-80) cc_final: 0.7581 (m-80) REVERT: C 178 PHE cc_start: 0.8266 (m-80) cc_final: 0.7653 (m-10) REVERT: C 179 TYR cc_start: 0.8429 (t80) cc_final: 0.8070 (t80) REVERT: C 239 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8368 (pp20) REVERT: C 240 LEU cc_start: 0.8014 (mt) cc_final: 0.7811 (mt) REVERT: D 18 THR cc_start: 0.6562 (p) cc_final: 0.6194 (p) REVERT: D 20 MET cc_start: 0.8768 (ppp) cc_final: 0.8506 (ppp) REVERT: D 46 TYR cc_start: 0.8716 (m-10) cc_final: 0.8217 (m-80) REVERT: D 56 MET cc_start: 0.2402 (mmm) cc_final: 0.2131 (mpp) REVERT: D 101 HIS cc_start: 0.4869 (m-70) cc_final: 0.4585 (m170) REVERT: D 131 LEU cc_start: 0.8339 (tt) cc_final: 0.8055 (mt) REVERT: D 149 ASP cc_start: 0.7743 (t0) cc_final: 0.7437 (t0) REVERT: D 174 TYR cc_start: 0.4060 (t80) cc_final: 0.3670 (t80) REVERT: D 204 TYR cc_start: 0.8718 (t80) cc_final: 0.8323 (t80) REVERT: D 281 ASP cc_start: 0.7973 (p0) cc_final: 0.7252 (t70) outliers start: 49 outliers final: 30 residues processed: 610 average time/residue: 0.1256 time to fit residues: 114.4271 Evaluate side-chains 577 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 543 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092897 restraints weight = 34973.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096292 restraints weight = 17261.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098450 restraints weight = 10511.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099815 restraints weight = 7389.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100807 restraints weight = 5775.171| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16299 Z= 0.196 Angle : 0.649 12.157 22004 Z= 0.343 Chirality : 0.044 0.200 2348 Planarity : 0.004 0.057 2812 Dihedral : 7.037 57.048 2265 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.27 % Allowed : 24.04 % Favored : 72.70 % 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: 1.09 (0.19), residues: 1928 helix: 1.21 (0.15), residues: 1144 sheet: -0.49 (0.39), residues: 150 loop : 0.35 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 196 TYR 0.022 0.002 TYR B 613 PHE 0.025 0.002 PHE B 491 TRP 0.021 0.002 TRP C 30 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (16298) covalent geometry : angle 0.64941 / 0.34 (22004) hydrogen bonds : bond 0.04107 / 2.60 ( 896) hydrogen bonds : angle 5.10956 / 3.54 ( 2616) Misc. bond : bond 0.00010 / 0.01 ( 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 611 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 555 time to evaluate : 0.555 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 178 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 218 ASN cc_start: 0.8795 (t0) cc_final: 0.8558 (t0) REVERT: A 312 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8507 (pt0) REVERT: A 322 MET cc_start: 0.8418 (tpp) cc_final: 0.7872 (tpp) REVERT: A 379 SER cc_start: 0.9297 (t) cc_final: 0.8988 (t) REVERT: A 383 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8590 (t) REVERT: A 406 ASP cc_start: 0.8106 (m-30) cc_final: 0.7768 (m-30) REVERT: A 485 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7663 (mtt90) REVERT: A 493 MET cc_start: 0.8935 (tmm) cc_final: 0.8462 (tmm) REVERT: A 640 MET cc_start: 0.9019 (tpp) cc_final: 0.8675 (tpp) REVERT: A 668 ASN cc_start: 0.8977 (m-40) cc_final: 0.8712 (m-40) REVERT: A 684 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: B 116 GLU cc_start: 0.8633 (mt-10) cc_final: 0.7996 (mp0) REVERT: B 200 SER cc_start: 0.8969 (t) cc_final: 0.8263 (t) REVERT: B 246 SER cc_start: 0.7536 (m) cc_final: 0.7305 (p) REVERT: B 250 TYR cc_start: 0.9199 (m-80) cc_final: 0.8180 (m-80) REVERT: B 348 MET cc_start: 0.7552 (tpp) cc_final: 0.7273 (tpp) REVERT: B 379 SER cc_start: 0.8861 (t) cc_final: 0.7759 (t) REVERT: B 480 GLU cc_start: 0.8733 (mp0) cc_final: 0.8371 (mp0) REVERT: B 515 ASP cc_start: 0.8973 (m-30) cc_final: 0.8739 (m-30) REVERT: B 550 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7438 (ttm) REVERT: B 632 MET cc_start: 0.9085 (mtp) cc_final: 0.8719 (mtm) REVERT: B 639 ASP cc_start: 0.8588 (m-30) cc_final: 0.7831 (m-30) REVERT: B 640 MET cc_start: 0.9106 (tpp) cc_final: 0.8789 (tpp) REVERT: B 670 ILE cc_start: 0.9294 (mm) cc_final: 0.9090 (mt) REVERT: B 677 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8727 (mmm-85) REVERT: B 686 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7831 (mtm-85) REVERT: C 56 MET cc_start: -0.4866 (tpt) cc_final: -0.5171 (tpp) REVERT: C 178 PHE cc_start: 0.8332 (m-10) cc_final: 0.7751 (m-10) REVERT: C 179 TYR cc_start: 0.8468 (t80) cc_final: 0.8108 (t80) REVERT: C 239 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8486 (pp20) REVERT: C 240 LEU cc_start: 0.7976 (mt) cc_final: 0.7736 (mt) REVERT: D 18 THR cc_start: 0.6678 (p) cc_final: 0.6303 (p) REVERT: D 20 MET cc_start: 0.8318 (ppp) cc_final: 0.8081 (ppp) REVERT: D 46 TYR cc_start: 0.8761 (m-10) cc_final: 0.8298 (m-80) REVERT: D 131 LEU cc_start: 0.8369 (tt) cc_final: 0.8138 (mt) REVERT: D 149 ASP cc_start: 0.7719 (t0) cc_final: 0.7379 (t0) REVERT: D 174 TYR cc_start: 0.4424 (t80) cc_final: 0.4056 (t80) REVERT: D 179 TYR cc_start: 0.8143 (t80) cc_final: 0.7817 (t80) REVERT: D 204 TYR cc_start: 0.8724 (t80) cc_final: 0.8399 (t80) REVERT: D 235 LEU cc_start: 0.8876 (mt) cc_final: 0.8641 (pp) REVERT: D 281 ASP cc_start: 0.8040 (p0) cc_final: 0.7538 (t70) outliers start: 56 outliers final: 37 residues processed: 583 average time/residue: 0.1215 time to fit residues: 106.1318 Evaluate side-chains 545 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 503 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 370 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.094001 restraints weight = 34640.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097390 restraints weight = 17078.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099562 restraints weight = 10374.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101021 restraints weight = 7307.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101935 restraints weight = 5696.687| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (15 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.6028 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= 0.155 Angle : 0.661 15.649 22004 Z= 0.343 Chirality : 0.043 0.183 2348 Planarity : 0.004 0.051 2812 Dihedral : 6.846 58.851 2264 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.92 % Allowed : 25.96 % Favored : 71.12 % 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: 0.98 (0.18), residues: 1928 helix: 1.15 (0.15), residues: 1142 sheet: -0.40 (0.40), residues: 134 loop : 0.19 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 196 TYR 0.022 0.001 TYR B 613 PHE 0.035 0.002 PHE D 92 TRP 0.027 0.002 TRP C 30 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (16298) covalent geometry : angle 0.66122 / 0.34 (22004) hydrogen bonds : bond 0.03988 / 2.52 ( 896) hydrogen bonds : angle 5.13375 / 3.56 ( 2616) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 538 time to evaluate : 0.621 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 31 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8547 (mp0) REVERT: A 128 PHE cc_start: 0.8936 (t80) cc_final: 0.8663 (t80) REVERT: A 218 ASN cc_start: 0.8870 (t0) cc_final: 0.8601 (t0) REVERT: A 312 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: A 350 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7955 (mtp180) REVERT: A 379 SER cc_start: 0.9296 (t) cc_final: 0.8971 (t) REVERT: A 383 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8554 (t) REVERT: A 406 ASP cc_start: 0.7947 (m-30) cc_final: 0.7580 (m-30) REVERT: A 485 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.7666 (mtt90) REVERT: A 493 MET cc_start: 0.8919 (tmm) cc_final: 0.8465 (tmm) REVERT: A 640 MET cc_start: 0.8992 (tpp) cc_final: 0.8664 (tpp) REVERT: A 684 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 31 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: B 200 SER cc_start: 0.8923 (t) cc_final: 0.8176 (t) REVERT: B 228 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8411 (tppt) REVERT: B 246 SER cc_start: 0.7554 (m) cc_final: 0.7340 (p) REVERT: B 250 TYR cc_start: 0.9219 (m-80) cc_final: 0.8286 (m-80) REVERT: B 276 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7882 (mptt) REVERT: B 348 MET cc_start: 0.7601 (tpp) cc_final: 0.7280 (tpp) REVERT: B 379 SER cc_start: 0.8868 (t) cc_final: 0.7793 (t) REVERT: B 394 TYR cc_start: 0.9156 (m-80) cc_final: 0.8881 (m-80) REVERT: B 480 GLU cc_start: 0.8810 (mp0) cc_final: 0.8466 (mp0) REVERT: B 515 ASP cc_start: 0.8967 (m-30) cc_final: 0.8718 (m-30) REVERT: B 632 MET cc_start: 0.9156 (mtp) cc_final: 0.8712 (mtm) REVERT: B 639 ASP cc_start: 0.8529 (m-30) cc_final: 0.7663 (m-30) REVERT: B 640 MET cc_start: 0.9116 (tpp) cc_final: 0.8747 (tpp) REVERT: B 646 GLN cc_start: 0.9096 (pt0) cc_final: 0.8739 (pm20) REVERT: B 686 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.7921 (mtm-85) REVERT: C 56 MET cc_start: -0.4919 (tpt) cc_final: -0.5232 (tpp) REVERT: C 178 PHE cc_start: 0.8393 (m-10) cc_final: 0.7811 (m-10) REVERT: C 179 TYR cc_start: 0.8502 (t80) cc_final: 0.8149 (t80) REVERT: D 18 THR cc_start: 0.6732 (p) cc_final: 0.6351 (p) REVERT: D 20 MET cc_start: 0.8350 (ppp) cc_final: 0.8088 (ppp) REVERT: D 46 TYR cc_start: 0.8771 (m-10) cc_final: 0.8324 (m-80) REVERT: D 131 LEU cc_start: 0.8394 (tt) cc_final: 0.8127 (mt) REVERT: D 149 ASP cc_start: 0.7631 (t0) cc_final: 0.7373 (t0) REVERT: D 174 TYR cc_start: 0.4389 (t80) cc_final: 0.3927 (t80) REVERT: D 179 TYR cc_start: 0.8220 (t80) cc_final: 0.7883 (t80) REVERT: D 204 TYR cc_start: 0.8790 (t80) cc_final: 0.8434 (t80) REVERT: D 252 LEU cc_start: 0.6942 (mm) cc_final: 0.6653 (mm) REVERT: D 281 ASP cc_start: 0.8117 (p0) cc_final: 0.7765 (t70) outliers start: 50 outliers final: 31 residues processed: 564 average time/residue: 0.1272 time to fit residues: 107.3375 Evaluate side-chains 549 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 514 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 568 HIS ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.132154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093373 restraints weight = 34847.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096679 restraints weight = 17386.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098844 restraints weight = 10558.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099950 restraints weight = 7441.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101049 restraints weight = 5997.693| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16299 Z= 0.200 Angle : 0.690 17.028 22004 Z= 0.359 Chirality : 0.045 0.475 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.951 59.385 2264 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.74 % Allowed : 26.60 % Favored : 70.65 % 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: 0.85 (0.19), residues: 1928 helix: 1.09 (0.15), residues: 1144 sheet: -0.70 (0.39), residues: 146 loop : 0.12 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 274 TYR 0.023 0.002 TYR B 613 PHE 0.034 0.002 PHE B 487 TRP 0.040 0.003 TRP D 124 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (16298) covalent geometry : angle 0.68953 / 0.36 (22004) hydrogen bonds : bond 0.04100 / 2.57 ( 896) hydrogen bonds : angle 5.20760 / 3.62 ( 2616) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 517 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.9017 (t80) cc_final: 0.8735 (t80) REVERT: A 164 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7406 (ptm-80) REVERT: A 184 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8518 (tpp80) REVERT: A 218 ASN cc_start: 0.8887 (t0) cc_final: 0.8642 (t0) REVERT: A 301 PHE cc_start: 0.9126 (m-10) cc_final: 0.8778 (m-10) REVERT: A 312 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8473 (pt0) REVERT: A 350 ARG cc_start: 0.8334 (mtp180) cc_final: 0.7997 (mtp180) REVERT: A 379 SER cc_start: 0.9294 (t) cc_final: 0.8969 (t) REVERT: A 383 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8556 (t) REVERT: A 406 ASP cc_start: 0.7955 (m-30) cc_final: 0.7597 (m-30) REVERT: A 485 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7631 (mtt90) REVERT: A 493 MET cc_start: 0.8942 (tmm) cc_final: 0.8467 (tmm) REVERT: A 550 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6424 (mtt) REVERT: A 640 MET cc_start: 0.9045 (tpp) cc_final: 0.8701 (tpp) REVERT: A 668 ASN cc_start: 0.9019 (m-40) cc_final: 0.8698 (m-40) REVERT: A 684 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 200 SER cc_start: 0.8935 (t) cc_final: 0.8241 (t) REVERT: B 228 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8372 (tppt) REVERT: B 250 TYR cc_start: 0.9278 (m-80) cc_final: 0.8312 (m-80) REVERT: B 348 MET cc_start: 0.7608 (tpp) cc_final: 0.7266 (tpp) REVERT: B 379 SER cc_start: 0.8854 (t) cc_final: 0.7771 (t) REVERT: B 394 TYR cc_start: 0.9137 (m-80) cc_final: 0.8845 (m-80) REVERT: B 467 ASN cc_start: 0.9246 (m-40) cc_final: 0.8878 (m-40) REVERT: B 480 GLU cc_start: 0.8801 (mp0) cc_final: 0.8479 (mp0) REVERT: B 515 ASP cc_start: 0.8996 (m-30) cc_final: 0.8727 (m-30) REVERT: B 599 GLU cc_start: 0.7878 (pt0) cc_final: 0.7608 (pt0) REVERT: B 602 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 632 MET cc_start: 0.9223 (mtp) cc_final: 0.8739 (mtm) REVERT: B 640 MET cc_start: 0.9139 (tpp) cc_final: 0.8935 (tpp) REVERT: B 686 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7941 (mtm-85) REVERT: C 24 GLN cc_start: 0.8665 (mt0) cc_final: 0.8410 (mp10) REVERT: C 56 MET cc_start: -0.4817 (tpt) cc_final: -0.5189 (tpp) REVERT: C 172 PHE cc_start: 0.7571 (m-10) cc_final: 0.7291 (m-10) REVERT: C 178 PHE cc_start: 0.8357 (m-10) cc_final: 0.7852 (m-10) REVERT: C 179 TYR cc_start: 0.8556 (t80) cc_final: 0.8145 (t80) REVERT: D 18 THR cc_start: 0.6421 (p) cc_final: 0.6071 (p) REVERT: D 20 MET cc_start: 0.8342 (ppp) cc_final: 0.8091 (ppp) REVERT: D 46 TYR cc_start: 0.8818 (m-10) cc_final: 0.8405 (m-80) REVERT: D 149 ASP cc_start: 0.7722 (t0) cc_final: 0.7466 (t0) REVERT: D 174 TYR cc_start: 0.4826 (t80) cc_final: 0.4547 (t80) REVERT: D 179 TYR cc_start: 0.8325 (t80) cc_final: 0.7922 (t80) REVERT: D 204 TYR cc_start: 0.8804 (t80) cc_final: 0.8509 (t80) REVERT: D 211 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8386 (pt0) REVERT: D 252 LEU cc_start: 0.7018 (mm) cc_final: 0.6596 (mm) REVERT: D 266 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8030 (mmmt) outliers start: 47 outliers final: 36 residues processed: 536 average time/residue: 0.1272 time to fit residues: 102.1467 Evaluate side-chains 535 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 495 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 122 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093872 restraints weight = 34980.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097183 restraints weight = 17209.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099281 restraints weight = 10518.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100774 restraints weight = 7439.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101653 restraints weight = 5810.489| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16299 Z= 0.198 Angle : 0.709 18.124 22004 Z= 0.369 Chirality : 0.047 0.559 2348 Planarity : 0.004 0.064 2812 Dihedral : 6.954 59.824 2264 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.80 % Allowed : 27.30 % Favored : 69.89 % 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: 0.76 (0.19), residues: 1928 helix: 1.02 (0.15), residues: 1145 sheet: -0.72 (0.40), residues: 146 loop : 0.07 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.023 0.002 TYR B 613 PHE 0.027 0.002 PHE B 487 TRP 0.051 0.003 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (16298) covalent geometry : angle 0.70914 / 0.37 (22004) hydrogen bonds : bond 0.04114 / 2.61 ( 896) hydrogen bonds : angle 5.21616 / 3.64 ( 2616) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 515 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 128 PHE cc_start: 0.9011 (t80) cc_final: 0.8748 (t80) REVERT: A 161 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7174 (ttm170) REVERT: A 164 ARG cc_start: 0.8089 (ptm-80) cc_final: 0.7404 (ptm-80) REVERT: A 182 ILE cc_start: 0.9316 (mt) cc_final: 0.9055 (mp) REVERT: A 184 ARG cc_start: 0.8818 (tpp-160) cc_final: 0.8510 (tpp80) REVERT: A 218 ASN cc_start: 0.8925 (t0) cc_final: 0.8666 (t0) REVERT: A 312 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: A 350 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7991 (mtp180) REVERT: A 379 SER cc_start: 0.9286 (t) cc_final: 0.8939 (t) REVERT: A 383 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8483 (t) REVERT: A 406 ASP cc_start: 0.8019 (m-30) cc_final: 0.7718 (m-30) REVERT: A 485 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7635 (mtt90) REVERT: A 493 MET cc_start: 0.8962 (tmm) cc_final: 0.8496 (tmm) REVERT: A 599 GLU cc_start: 0.8124 (mp0) cc_final: 0.7692 (mp0) REVERT: A 640 MET cc_start: 0.9041 (tpp) cc_final: 0.8693 (tpp) REVERT: A 668 ASN cc_start: 0.9020 (m-40) cc_final: 0.8691 (m110) REVERT: A 681 THR cc_start: 0.8986 (p) cc_final: 0.8660 (p) REVERT: A 684 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 31 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: B 65 GLU cc_start: 0.8290 (mp0) cc_final: 0.7524 (mp0) REVERT: B 116 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8140 (mp0) REVERT: B 161 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7514 (mtt180) REVERT: B 200 SER cc_start: 0.8954 (t) cc_final: 0.8325 (t) REVERT: B 228 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8343 (mmtt) REVERT: B 250 TYR cc_start: 0.9271 (m-80) cc_final: 0.8423 (m-80) REVERT: B 348 MET cc_start: 0.7602 (tpp) cc_final: 0.7268 (tpp) REVERT: B 379 SER cc_start: 0.8823 (t) cc_final: 0.7967 (t) REVERT: B 467 ASN cc_start: 0.9226 (m-40) cc_final: 0.8874 (m-40) REVERT: B 480 GLU cc_start: 0.8788 (mp0) cc_final: 0.8453 (mp0) REVERT: B 515 ASP cc_start: 0.9000 (m-30) cc_final: 0.8689 (m-30) REVERT: B 602 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 610 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8486 (mmmm) REVERT: B 632 MET cc_start: 0.9178 (mtp) cc_final: 0.8545 (mtm) REVERT: B 686 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.7990 (mtm-85) REVERT: C 24 GLN cc_start: 0.8748 (mt0) cc_final: 0.8358 (mp10) REVERT: C 56 MET cc_start: -0.4845 (tpt) cc_final: -0.5222 (tpp) REVERT: C 137 MET cc_start: 0.3921 (mmm) cc_final: 0.3644 (mpp) REVERT: C 172 PHE cc_start: 0.7605 (m-10) cc_final: 0.7320 (m-10) REVERT: C 178 PHE cc_start: 0.8369 (m-10) cc_final: 0.7897 (m-10) REVERT: C 179 TYR cc_start: 0.8591 (t80) cc_final: 0.8188 (t80) REVERT: D 18 THR cc_start: 0.6747 (p) cc_final: 0.6337 (p) REVERT: D 20 MET cc_start: 0.8326 (ppp) cc_final: 0.8064 (ppp) REVERT: D 46 TYR cc_start: 0.8820 (m-10) cc_final: 0.8415 (m-80) REVERT: D 74 MET cc_start: 0.5689 (tmm) cc_final: 0.4410 (ppp) REVERT: D 131 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7714 (mt) REVERT: D 137 MET cc_start: 0.8460 (mmp) cc_final: 0.7730 (mtp) REVERT: D 142 TYR cc_start: 0.8277 (m-80) cc_final: 0.7906 (t80) REVERT: D 149 ASP cc_start: 0.7847 (t0) cc_final: 0.7618 (t0) REVERT: D 179 TYR cc_start: 0.8295 (t80) cc_final: 0.7908 (t80) REVERT: D 204 TYR cc_start: 0.8801 (t80) cc_final: 0.8524 (t80) REVERT: D 211 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8428 (pt0) REVERT: D 242 TYR cc_start: 0.7421 (t80) cc_final: 0.6952 (m-80) outliers start: 48 outliers final: 37 residues processed: 535 average time/residue: 0.1281 time to fit residues: 102.6727 Evaluate side-chains 519 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 477 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093505 restraints weight = 35223.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096902 restraints weight = 17417.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099053 restraints weight = 10539.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100507 restraints weight = 7406.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101424 restraints weight = 5749.678| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16299 Z= 0.166 Angle : 0.707 17.143 22004 Z= 0.367 Chirality : 0.046 0.483 2348 Planarity : 0.004 0.051 2812 Dihedral : 6.861 59.714 2264 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.51 % Allowed : 27.95 % Favored : 69.54 % 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: 0.72 (0.19), residues: 1928 helix: 0.99 (0.15), residues: 1148 sheet: -0.58 (0.42), residues: 134 loop : -0.00 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 274 TYR 0.024 0.001 TYR B 613 PHE 0.042 0.002 PHE B 487 TRP 0.046 0.003 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16298) covalent geometry : angle 0.70683 / 0.37 (22004) hydrogen bonds : bond 0.04141 / 2.62 ( 896) hydrogen bonds : angle 5.19944 / 3.63 ( 2616) Misc. bond : bond 0.00007 / 0.00 ( 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 549 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 506 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7595 (pt0) REVERT: A 128 PHE cc_start: 0.8955 (t80) cc_final: 0.8711 (t80) REVERT: A 161 ARG cc_start: 0.7618 (ttm170) cc_final: 0.7129 (ttm170) REVERT: A 164 ARG cc_start: 0.8042 (ptm-80) cc_final: 0.7426 (ptm-80) REVERT: A 182 ILE cc_start: 0.9316 (mt) cc_final: 0.9052 (mp) REVERT: A 218 ASN cc_start: 0.8954 (t0) cc_final: 0.8697 (t0) REVERT: A 301 PHE cc_start: 0.9144 (m-10) cc_final: 0.8751 (m-10) REVERT: A 312 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: A 350 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7934 (mtp180) REVERT: A 379 SER cc_start: 0.9276 (t) cc_final: 0.8961 (t) REVERT: A 383 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8562 (t) REVERT: A 485 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7611 (mtt90) REVERT: A 493 MET cc_start: 0.8989 (tmm) cc_final: 0.8504 (tmm) REVERT: A 599 GLU cc_start: 0.8122 (mp0) cc_final: 0.7670 (mp0) REVERT: A 640 MET cc_start: 0.9028 (tpp) cc_final: 0.8692 (tpp) REVERT: A 668 ASN cc_start: 0.8998 (m-40) cc_final: 0.8642 (m-40) REVERT: A 684 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: B 65 GLU cc_start: 0.8287 (mp0) cc_final: 0.7570 (mp0) REVERT: B 116 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8131 (mp0) REVERT: B 200 SER cc_start: 0.8901 (t) cc_final: 0.8267 (t) REVERT: B 228 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8321 (mmtt) REVERT: B 250 TYR cc_start: 0.9264 (m-80) cc_final: 0.8408 (m-80) REVERT: B 344 GLU cc_start: 0.8672 (tt0) cc_final: 0.8440 (tp30) REVERT: B 348 MET cc_start: 0.7662 (tpp) cc_final: 0.7323 (tpp) REVERT: B 362 ASP cc_start: 0.7899 (m-30) cc_final: 0.7473 (m-30) REVERT: B 379 SER cc_start: 0.8828 (t) cc_final: 0.7930 (t) REVERT: B 394 TYR cc_start: 0.9107 (m-80) cc_final: 0.8808 (m-80) REVERT: B 467 ASN cc_start: 0.9208 (m-40) cc_final: 0.8933 (m-40) REVERT: B 480 GLU cc_start: 0.8753 (mp0) cc_final: 0.8386 (mp0) REVERT: B 515 ASP cc_start: 0.8968 (m-30) cc_final: 0.8611 (m-30) REVERT: B 602 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 610 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8552 (mmmm) REVERT: B 632 MET cc_start: 0.9202 (mtp) cc_final: 0.8614 (mtm) REVERT: B 646 GLN cc_start: 0.9120 (pt0) cc_final: 0.8737 (pm20) REVERT: B 677 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8030 (ttm-80) REVERT: B 686 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8070 (mtm-85) REVERT: C 24 GLN cc_start: 0.8652 (mt0) cc_final: 0.8359 (mp10) REVERT: C 56 MET cc_start: -0.5024 (tpt) cc_final: -0.5421 (tpp) REVERT: C 64 LEU cc_start: 0.6402 (tp) cc_final: 0.5765 (pp) REVERT: C 172 PHE cc_start: 0.7486 (m-10) cc_final: 0.7222 (m-80) REVERT: C 178 PHE cc_start: 0.8362 (m-10) cc_final: 0.7939 (m-10) REVERT: C 179 TYR cc_start: 0.8578 (t80) cc_final: 0.8180 (t80) REVERT: D 18 THR cc_start: 0.6416 (p) cc_final: 0.6145 (p) REVERT: D 20 MET cc_start: 0.8322 (ppp) cc_final: 0.8043 (ppp) REVERT: D 137 MET cc_start: 0.8522 (mmp) cc_final: 0.7853 (mtp) REVERT: D 149 ASP cc_start: 0.7875 (t0) cc_final: 0.7596 (t0) REVERT: D 204 TYR cc_start: 0.8825 (t80) cc_final: 0.8542 (t80) REVERT: D 266 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7867 (mmmt) REVERT: D 269 MET cc_start: 0.8873 (ppp) cc_final: 0.8535 (ppp) outliers start: 43 outliers final: 35 residues processed: 525 average time/residue: 0.1320 time to fit residues: 103.0987 Evaluate side-chains 514 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 476 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094804 restraints weight = 35304.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098183 restraints weight = 17223.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100296 restraints weight = 10394.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101836 restraints weight = 7336.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102672 restraints weight = 5646.237| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16299 Z= 0.147 Angle : 0.743 21.255 22004 Z= 0.381 Chirality : 0.046 0.541 2348 Planarity : 0.004 0.054 2812 Dihedral : 6.762 59.071 2264 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.10 % Allowed : 28.65 % Favored : 69.25 % 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: 0.70 (0.19), residues: 1928 helix: 0.97 (0.15), residues: 1147 sheet: -0.63 (0.42), residues: 136 loop : -0.01 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 274 TYR 0.036 0.001 TYR C 142 PHE 0.028 0.002 PHE B 487 TRP 0.055 0.003 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16298) covalent geometry : angle 0.74339 / 0.38 (22004) hydrogen bonds : bond 0.04122 / 2.59 ( 896) hydrogen bonds : angle 5.21261 / 3.63 ( 2616) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 526 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8466 (mp0) REVERT: A 128 PHE cc_start: 0.8928 (t80) cc_final: 0.8686 (t80) REVERT: A 161 ARG cc_start: 0.7604 (ttm170) cc_final: 0.7149 (ttm170) REVERT: A 164 ARG cc_start: 0.8099 (ptm-80) cc_final: 0.7466 (ptm-80) REVERT: A 182 ILE cc_start: 0.9305 (mt) cc_final: 0.9047 (mp) REVERT: A 218 ASN cc_start: 0.8917 (t0) cc_final: 0.8650 (t0) REVERT: A 301 PHE cc_start: 0.9125 (m-10) cc_final: 0.8842 (m-10) REVERT: A 312 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: A 350 ARG cc_start: 0.8294 (mtp180) cc_final: 0.7962 (mtp180) REVERT: A 383 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8634 (t) REVERT: A 385 VAL cc_start: 0.9105 (t) cc_final: 0.8633 (p) REVERT: A 485 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7840 (mtt90) REVERT: A 493 MET cc_start: 0.9001 (tmm) cc_final: 0.8655 (tmm) REVERT: A 599 GLU cc_start: 0.8114 (mp0) cc_final: 0.7674 (mp0) REVERT: A 640 MET cc_start: 0.9005 (tpp) cc_final: 0.8701 (tpp) REVERT: A 668 ASN cc_start: 0.8951 (m-40) cc_final: 0.8632 (m-40) REVERT: A 684 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: B 116 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8115 (mp0) REVERT: B 200 SER cc_start: 0.8905 (t) cc_final: 0.8257 (t) REVERT: B 228 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8268 (mmtt) REVERT: B 250 TYR cc_start: 0.9245 (m-80) cc_final: 0.8400 (m-80) REVERT: B 348 MET cc_start: 0.7646 (tpp) cc_final: 0.7286 (tpp) REVERT: B 362 ASP cc_start: 0.7904 (m-30) cc_final: 0.7468 (m-30) REVERT: B 379 SER cc_start: 0.8819 (t) cc_final: 0.7891 (t) REVERT: B 394 TYR cc_start: 0.9104 (m-80) cc_final: 0.8818 (m-80) REVERT: B 452 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7993 (ttm170) REVERT: B 458 MET cc_start: 0.8593 (mtp) cc_final: 0.8387 (ttm) REVERT: B 467 ASN cc_start: 0.9168 (m-40) cc_final: 0.8919 (m-40) REVERT: B 480 GLU cc_start: 0.8770 (mp0) cc_final: 0.8391 (mp0) REVERT: B 515 ASP cc_start: 0.8936 (m-30) cc_final: 0.8568 (m-30) REVERT: B 602 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 610 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8633 (mmmm) REVERT: B 632 MET cc_start: 0.9194 (mtp) cc_final: 0.8600 (mtm) REVERT: B 646 GLN cc_start: 0.9139 (pt0) cc_final: 0.8743 (pm20) REVERT: B 677 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8320 (ttm-80) REVERT: B 686 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8091 (mtm-85) REVERT: C 56 MET cc_start: -0.5061 (tpt) cc_final: -0.5421 (tpp) REVERT: C 64 LEU cc_start: 0.6292 (tp) cc_final: 0.5640 (pp) REVERT: C 178 PHE cc_start: 0.8406 (m-10) cc_final: 0.7986 (m-10) REVERT: C 179 TYR cc_start: 0.8524 (t80) cc_final: 0.8142 (t80) REVERT: D 18 THR cc_start: 0.6342 (p) cc_final: 0.6102 (p) REVERT: D 20 MET cc_start: 0.8301 (ppp) cc_final: 0.8035 (ppp) REVERT: D 131 LEU cc_start: 0.8618 (mt) cc_final: 0.8394 (mt) REVERT: D 137 MET cc_start: 0.8556 (mmp) cc_final: 0.7914 (mtp) REVERT: D 142 TYR cc_start: 0.8275 (m-80) cc_final: 0.7906 (t80) REVERT: D 149 ASP cc_start: 0.7833 (t0) cc_final: 0.7626 (t0) REVERT: D 204 TYR cc_start: 0.8777 (t80) cc_final: 0.8515 (t80) REVERT: D 266 LYS cc_start: 0.8363 (mmmt) cc_final: 0.8017 (mmmt) REVERT: D 269 MET cc_start: 0.8971 (ppp) cc_final: 0.8694 (ppp) outliers start: 36 outliers final: 30 residues processed: 540 average time/residue: 0.1296 time to fit residues: 104.6446 Evaluate side-chains 533 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 499 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 30.0000 chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093706 restraints weight = 35364.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096889 restraints weight = 17431.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099103 restraints weight = 10863.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100511 restraints weight = 7572.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101559 restraints weight = 5896.551| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16299 Z= 0.174 Angle : 0.743 17.358 22004 Z= 0.386 Chirality : 0.046 0.490 2348 Planarity : 0.004 0.056 2812 Dihedral : 6.814 58.940 2264 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.28 % Allowed : 28.88 % Favored : 68.84 % 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: 0.69 (0.19), residues: 1928 helix: 0.98 (0.15), residues: 1138 sheet: -0.69 (0.42), residues: 140 loop : 0.00 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 274 TYR 0.033 0.002 TYR B 613 PHE 0.042 0.002 PHE C 172 TRP 0.052 0.003 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (16298) covalent geometry : angle 0.74344 / 0.39 (22004) hydrogen bonds : bond 0.04192 / 2.65 ( 896) hydrogen bonds : angle 5.26873 / 3.68 ( 2616) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.87 seconds wall clock time: 58 minutes 4.67 seconds (3484.67 seconds total)