Starting phenix.real_space_refine on Thu Aug 6 14:51:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx9_45000/08_2026/9bx9_45000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx9_45000/08_2026/9bx9_45000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx9_45000/08_2026/9bx9_45000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx9_45000/08_2026/9bx9_45000.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx9_45000/08_2026/9bx9_45000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx9_45000/08_2026/9bx9_45000_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.46, per 1000 atoms: 0.22 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 127.75, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 658.6 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: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A 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: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.638A 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: 6.055A 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: 4.274A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.950A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.722A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A 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: 3.567A 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: 4.874A 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: 6.313A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.059A 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: 6.457A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A 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: 2.90 Time building geometry restraints manager: 1.76 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: 4959 1.34 - 1.46: 2935 1.46 - 1.58: 8229 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 1.608 0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.36e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.17e+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: 21468 2.11 - 4.23: 464 4.23 - 6.34: 57 6.34 - 8.46: 8 8.46 - 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 110.54 116.58 -6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+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 ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8640 17.66 - 35.31: 858 35.31 - 52.97: 253 52.97 - 70.62: 65 70.62 - 88.28: 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 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+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 -134.37 11.77 0 2.50e+00 1.60e-01 2.22e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2126 0.094 - 0.188: 183 0.188 - 0.282: 34 0.282 - 0.376: 3 0.376 - 0.470: 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 5.52e+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 4.55e+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 2.16 0.35 2.00e-01 2.50e+01 2.99e+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 4.15e-02 2.76e+00 pdb=" N PRO D 75 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 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 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11864 3.11 - 3.70: 26403 3.70 - 4.30: 41201 4.30 - 4.90: 64928 Nonbonded interactions: 144527 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.918 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.430 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.833 16299 Z= 0.732 Angle : 0.756 10.570 22004 Z= 0.461 Chirality : 0.059 0.470 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.909 88.276 6168 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 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 0.75590 / 0.46 (22004) hydrogen bonds : bond 0.16168 / 10.52 ( 896) hydrogen bonds : angle 6.35121 / 4.47 ( 2616) Misc. bond : bond 0.83310 / 43.85 ( 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 718 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 694 time to evaluate : 0.666 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 27 ASP cc_start: 0.7273 (p0) cc_final: 0.6877 (p0) REVERT: A 30 LYS cc_start: 0.8021 (tptt) cc_final: 0.7771 (tppt) REVERT: A 119 GLU cc_start: 0.7911 (mp0) cc_final: 0.7527 (mp0) REVERT: A 157 LEU cc_start: 0.9234 (tp) cc_final: 0.8950 (tt) REVERT: A 177 ASP cc_start: 0.8784 (t0) cc_final: 0.8268 (t0) REVERT: A 179 LEU cc_start: 0.9223 (tp) cc_final: 0.8934 (tp) REVERT: A 188 ILE cc_start: 0.9187 (mt) cc_final: 0.8972 (mt) REVERT: A 232 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (m-40) REVERT: A 240 MET cc_start: 0.5912 (tpt) cc_final: 0.5632 (tpt) REVERT: A 262 LEU cc_start: 0.8711 (mt) cc_final: 0.8291 (mt) REVERT: A 362 ASP cc_start: 0.6953 (m-30) cc_final: 0.6564 (m-30) REVERT: A 379 SER cc_start: 0.9068 (t) cc_final: 0.8363 (t) REVERT: A 447 ASN cc_start: 0.8098 (m-40) cc_final: 0.7889 (m-40) REVERT: A 458 MET cc_start: 0.8982 (mmm) cc_final: 0.8567 (mmt) REVERT: A 494 MET cc_start: 0.7915 (mtp) cc_final: 0.7678 (mtp) REVERT: A 584 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8550 (tp) REVERT: A 591 THR cc_start: 0.9175 (p) cc_final: 0.8844 (m) REVERT: A 597 ILE cc_start: 0.9307 (pt) cc_final: 0.9059 (pt) REVERT: A 598 MET cc_start: 0.7733 (mtm) cc_final: 0.7475 (mtm) REVERT: A 654 PHE cc_start: 0.8807 (t80) cc_final: 0.8465 (t80) REVERT: B 104 TYR cc_start: 0.7947 (m-80) cc_final: 0.7483 (m-80) REVERT: B 172 LEU cc_start: 0.9169 (mp) cc_final: 0.8671 (mp) REVERT: B 177 ASP cc_start: 0.8208 (t0) cc_final: 0.7740 (t0) REVERT: B 362 ASP cc_start: 0.7489 (m-30) cc_final: 0.6735 (m-30) REVERT: B 425 ILE cc_start: 0.8789 (mt) cc_final: 0.8575 (mt) REVERT: B 494 MET cc_start: 0.7901 (mtp) cc_final: 0.7694 (mtm) REVERT: B 496 ASN cc_start: 0.9058 (t0) cc_final: 0.8828 (t0) REVERT: B 501 GLN cc_start: 0.8121 (tt0) cc_final: 0.7812 (tt0) REVERT: B 550 MET cc_start: 0.8658 (ttm) cc_final: 0.8132 (mtm) REVERT: B 612 TYR cc_start: 0.7092 (m-80) cc_final: 0.6643 (m-80) REVERT: C 137 MET cc_start: -0.1845 (mtp) cc_final: -0.3140 (mmm) REVERT: C 287 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.1106 (tp) REVERT: D 137 MET cc_start: -0.1437 (mtp) cc_final: -0.3367 (mmt) REVERT: D 282 ILE cc_start: -0.0509 (OUTLIER) cc_final: -0.1113 (mt) outliers start: 24 outliers final: 5 residues processed: 712 average time/residue: 0.1410 time to fit residues: 147.7230 Evaluate side-chains 456 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 447 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS 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: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 14 ASN A 320 ASN A 370 ASN A 645 GLN A 668 ASN B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 418 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 19 GLN C 28 GLN C 91 ASN C 216 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 146 GLN D 233 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.166575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100531 restraints weight = 29672.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103947 restraints weight = 14075.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106151 restraints weight = 8628.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107608 restraints weight = 6227.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108322 restraints weight = 4901.210| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16299 Z= 0.262 Angle : 0.646 10.603 22004 Z= 0.351 Chirality : 0.044 0.213 2348 Planarity : 0.004 0.050 2812 Dihedral : 7.470 64.013 2280 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.33 % Allowed : 15.17 % Favored : 81.51 % 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: 1.74 (0.19), residues: 1928 helix: 1.64 (0.15), residues: 1129 sheet: 0.16 (0.40), residues: 136 loop : 0.72 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.021 0.002 TYR C 22 PHE 0.029 0.002 PHE A 261 TRP 0.022 0.003 TRP D 124 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (16298) covalent geometry : angle 0.64618 / 0.35 (22004) hydrogen bonds : bond 0.04820 / 3.05 ( 896) hydrogen bonds : angle 5.08365 / 3.52 ( 2616) Misc. bond : bond 0.00119 / 0.06 ( 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 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 464 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8844 (mp0) cc_final: 0.8598 (mp0) REVERT: A 148 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8418 (mt-10) REVERT: A 174 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 177 ASP cc_start: 0.8907 (t0) cc_final: 0.8638 (t0) REVERT: A 250 TYR cc_start: 0.8880 (m-80) cc_final: 0.8194 (m-80) REVERT: A 362 ASP cc_start: 0.7752 (m-30) cc_final: 0.7113 (m-30) REVERT: A 379 SER cc_start: 0.8956 (t) cc_final: 0.8307 (t) REVERT: A 493 MET cc_start: 0.9216 (tmm) cc_final: 0.8674 (tmm) REVERT: A 494 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8919 (mtp) REVERT: A 584 ILE cc_start: 0.9464 (tp) cc_final: 0.9219 (tp) REVERT: A 686 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7741 (mtt90) REVERT: B 104 TYR cc_start: 0.8877 (m-80) cc_final: 0.8075 (m-80) REVERT: B 109 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8475 (m-40) REVERT: B 135 GLU cc_start: 0.8353 (mp0) cc_final: 0.8057 (mp0) REVERT: B 177 ASP cc_start: 0.8149 (t0) cc_final: 0.7762 (t0) REVERT: B 181 ASP cc_start: 0.8753 (m-30) cc_final: 0.8477 (m-30) REVERT: B 276 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8625 (mmtm) REVERT: B 334 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8865 (pttm) REVERT: B 362 ASP cc_start: 0.8390 (m-30) cc_final: 0.8084 (m-30) REVERT: B 586 TYR cc_start: 0.8762 (m-80) cc_final: 0.8501 (m-80) REVERT: B 612 TYR cc_start: 0.8383 (m-80) cc_final: 0.7770 (m-80) REVERT: B 640 MET cc_start: 0.9012 (tpp) cc_final: 0.8638 (tpp) REVERT: C 137 MET cc_start: -0.4895 (mtp) cc_final: -0.5416 (mmm) REVERT: C 205 VAL cc_start: 0.4238 (t) cc_final: 0.3638 (m) REVERT: C 235 LEU cc_start: 0.7721 (mt) cc_final: 0.7503 (mt) REVERT: C 287 LEU cc_start: 0.0099 (OUTLIER) cc_final: -0.0575 (tp) REVERT: D 110 MET cc_start: 0.5171 (mtt) cc_final: 0.4734 (tmm) REVERT: D 185 MET cc_start: 0.6109 (mmm) cc_final: 0.5727 (mmm) outliers start: 57 outliers final: 35 residues processed: 498 average time/residue: 0.1270 time to fit residues: 95.4344 Evaluate side-chains 427 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 239 GLN A 370 ASN B 62 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN C 24 GLN C 84 HIS D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103251 restraints weight = 29953.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106904 restraints weight = 13940.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108989 restraints weight = 8465.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110511 restraints weight = 6031.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111494 restraints weight = 4710.456| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16299 Z= 0.136 Angle : 0.566 8.635 22004 Z= 0.304 Chirality : 0.041 0.159 2348 Planarity : 0.003 0.049 2812 Dihedral : 7.064 59.475 2273 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.80 % Allowed : 17.44 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.18), residues: 1928 helix: 1.68 (0.15), residues: 1131 sheet: 0.79 (0.41), residues: 118 loop : 0.57 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.022 0.001 TYR C 179 PHE 0.023 0.001 PHE A 261 TRP 0.023 0.001 TRP D 124 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (16298) covalent geometry : angle 0.56598 / 0.30 (22004) hydrogen bonds : bond 0.04154 / 2.63 ( 896) hydrogen bonds : angle 4.86220 / 3.38 ( 2616) Misc. bond : bond 0.00057 / 0.03 ( 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 510 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 462 time to evaluate : 0.616 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: A 27 ASP cc_start: 0.8226 (p0) cc_final: 0.7981 (p0) REVERT: A 30 LYS cc_start: 0.9310 (tppt) cc_final: 0.8959 (tppt) REVERT: A 119 GLU cc_start: 0.8882 (mp0) cc_final: 0.8546 (mp0) REVERT: A 157 LEU cc_start: 0.9338 (tp) cc_final: 0.9114 (tp) REVERT: A 164 ARG cc_start: 0.8293 (ptt90) cc_final: 0.7951 (ptt90) REVERT: A 232 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: A 250 TYR cc_start: 0.8931 (m-80) cc_final: 0.8184 (m-80) REVERT: A 334 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8598 (ptpt) REVERT: A 362 ASP cc_start: 0.7851 (m-30) cc_final: 0.7429 (m-30) REVERT: A 379 SER cc_start: 0.9088 (t) cc_final: 0.8419 (t) REVERT: A 493 MET cc_start: 0.9283 (tmm) cc_final: 0.8658 (tmm) REVERT: A 640 MET cc_start: 0.9275 (tpp) cc_final: 0.8970 (tpp) REVERT: A 654 PHE cc_start: 0.9112 (t80) cc_final: 0.8905 (t80) REVERT: A 686 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7793 (mtt90) REVERT: B 8 LYS cc_start: 0.8708 (tppt) cc_final: 0.8496 (tppt) REVERT: B 135 GLU cc_start: 0.8318 (mp0) cc_final: 0.8022 (mp0) REVERT: B 147 GLN cc_start: 0.9167 (mt0) cc_final: 0.8914 (mm-40) REVERT: B 232 ASN cc_start: 0.9019 (t0) cc_final: 0.8801 (m-40) REVERT: B 276 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8515 (mmtm) REVERT: B 334 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8807 (pttm) REVERT: B 483 GLU cc_start: 0.8754 (mp0) cc_final: 0.8227 (pm20) REVERT: B 526 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7506 (tp30) REVERT: B 586 TYR cc_start: 0.8622 (m-80) cc_final: 0.8248 (m-80) REVERT: B 640 MET cc_start: 0.9061 (tpp) cc_final: 0.8634 (tpp) REVERT: C 137 MET cc_start: -0.4647 (mtp) cc_final: -0.5435 (mmm) REVERT: C 235 LEU cc_start: 0.7812 (mt) cc_final: 0.7472 (mt) REVERT: C 287 LEU cc_start: 0.0319 (OUTLIER) cc_final: -0.0045 (tp) REVERT: D 110 MET cc_start: 0.5344 (mtt) cc_final: 0.5013 (tmm) REVERT: D 137 MET cc_start: -0.6357 (ptp) cc_final: -0.7358 (tpp) REVERT: D 185 MET cc_start: 0.6387 (mmm) cc_final: 0.6048 (mmm) outliers start: 48 outliers final: 26 residues processed: 484 average time/residue: 0.1273 time to fit residues: 93.4355 Evaluate side-chains 442 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 412 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098504 restraints weight = 30053.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101912 restraints weight = 14200.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104021 restraints weight = 8757.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105360 restraints weight = 6305.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106278 restraints weight = 4953.070| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16299 Z= 0.244 Angle : 0.611 9.068 22004 Z= 0.326 Chirality : 0.043 0.211 2348 Planarity : 0.004 0.055 2812 Dihedral : 7.167 56.320 2268 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.27 % Allowed : 17.97 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 1928 helix: 1.60 (0.15), residues: 1133 sheet: -0.43 (0.39), residues: 146 loop : 0.68 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.018 0.001 TYR C 22 PHE 0.020 0.002 PHE A 261 TRP 0.028 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (16298) covalent geometry : angle 0.61051 / 0.33 (22004) hydrogen bonds : bond 0.04063 / 2.59 ( 896) hydrogen bonds : angle 4.93612 / 3.44 ( 2616) Misc. bond : bond 0.00371 / 0.20 ( 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 471 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 415 time to evaluate : 0.612 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: A 30 LYS cc_start: 0.9364 (tppt) cc_final: 0.9017 (tppt) REVERT: A 119 GLU cc_start: 0.8933 (mp0) cc_final: 0.8575 (mp0) REVERT: A 178 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 250 TYR cc_start: 0.8979 (m-80) cc_final: 0.8192 (m-80) REVERT: A 362 ASP cc_start: 0.7799 (m-30) cc_final: 0.7512 (m-30) REVERT: A 379 SER cc_start: 0.8950 (t) cc_final: 0.8282 (t) REVERT: A 493 MET cc_start: 0.9268 (tmm) cc_final: 0.8560 (tmm) REVERT: A 657 PHE cc_start: 0.9101 (m-80) cc_final: 0.8867 (m-80) REVERT: A 686 ARG cc_start: 0.8116 (mmt-90) cc_final: 0.7738 (mtt90) REVERT: B 8 LYS cc_start: 0.8770 (tppt) cc_final: 0.8561 (tppt) REVERT: B 104 TYR cc_start: 0.8982 (m-80) cc_final: 0.8142 (m-80) REVERT: B 135 GLU cc_start: 0.8304 (mp0) cc_final: 0.7941 (mp0) REVERT: B 147 GLN cc_start: 0.9307 (mt0) cc_final: 0.8995 (mm-40) REVERT: B 334 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8960 (pttm) REVERT: B 348 MET cc_start: 0.8207 (tmm) cc_final: 0.7965 (tmm) REVERT: B 483 GLU cc_start: 0.8791 (mp0) cc_final: 0.8466 (pm20) REVERT: B 526 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7513 (tp30) REVERT: B 586 TYR cc_start: 0.8702 (m-80) cc_final: 0.8261 (m-80) REVERT: B 640 MET cc_start: 0.8986 (tpp) cc_final: 0.8569 (tpp) REVERT: C 137 MET cc_start: -0.4726 (mtp) cc_final: -0.5467 (mmm) REVERT: C 231 LEU cc_start: 0.1696 (OUTLIER) cc_final: 0.1222 (pp) REVERT: C 235 LEU cc_start: 0.7725 (mt) cc_final: 0.7481 (mm) REVERT: C 287 LEU cc_start: 0.0621 (OUTLIER) cc_final: 0.0030 (tp) REVERT: D 110 MET cc_start: 0.5395 (mtt) cc_final: 0.4824 (tmm) REVERT: D 137 MET cc_start: -0.6305 (ptp) cc_final: -0.7395 (tpp) REVERT: D 185 MET cc_start: 0.6636 (mmm) cc_final: 0.6367 (mmm) outliers start: 56 outliers final: 38 residues processed: 443 average time/residue: 0.1244 time to fit residues: 83.8564 Evaluate side-chains 412 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 370 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 164 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 107 optimal weight: 0.0870 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101174 restraints weight = 29899.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104598 restraints weight = 13981.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106700 restraints weight = 8579.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108038 restraints weight = 6093.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109034 restraints weight = 4827.659| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16299 Z= 0.163 Angle : 0.558 9.684 22004 Z= 0.301 Chirality : 0.041 0.211 2348 Planarity : 0.003 0.056 2812 Dihedral : 7.066 54.368 2268 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.80 % Allowed : 19.89 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1928 helix: 1.54 (0.15), residues: 1131 sheet: -0.28 (0.39), residues: 140 loop : 0.58 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 274 TYR 0.014 0.001 TYR C 22 PHE 0.019 0.001 PHE A 261 TRP 0.027 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16298) covalent geometry : angle 0.55765 / 0.30 (22004) hydrogen bonds : bond 0.03867 / 2.45 ( 896) hydrogen bonds : angle 4.84597 / 3.38 ( 2616) Misc. bond : bond 0.00146 / 0.08 ( 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 445 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: A 119 GLU cc_start: 0.8874 (mp0) cc_final: 0.8534 (mp0) REVERT: A 161 ARG cc_start: 0.7824 (ttm170) cc_final: 0.6934 (ttm170) REVERT: A 232 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8194 (m110) REVERT: A 250 TYR cc_start: 0.8894 (m-80) cc_final: 0.8179 (m-80) REVERT: A 274 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7621 (tpp-160) REVERT: A 379 SER cc_start: 0.9019 (t) cc_final: 0.8313 (t) REVERT: A 384 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: A 466 MET cc_start: 0.9319 (ptm) cc_final: 0.9031 (ptp) REVERT: A 493 MET cc_start: 0.9290 (tmm) cc_final: 0.8600 (tmm) REVERT: A 586 TYR cc_start: 0.8870 (m-10) cc_final: 0.8573 (m-10) REVERT: A 640 MET cc_start: 0.9303 (tpp) cc_final: 0.8992 (tpp) REVERT: B 15 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8650 (mt-10) REVERT: B 135 GLU cc_start: 0.8311 (mp0) cc_final: 0.7955 (mp0) REVERT: B 147 GLN cc_start: 0.9252 (mt0) cc_final: 0.8962 (mm-40) REVERT: B 406 ASP cc_start: 0.8005 (m-30) cc_final: 0.7581 (t0) REVERT: B 415 ASN cc_start: 0.9367 (t0) cc_final: 0.9166 (t0) REVERT: B 526 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7459 (tp30) REVERT: B 590 SER cc_start: 0.9566 (t) cc_final: 0.8821 (p) REVERT: B 640 MET cc_start: 0.9011 (tpp) cc_final: 0.8564 (tpp) REVERT: C 129 LYS cc_start: 0.7688 (tptp) cc_final: 0.6641 (ptmt) REVERT: C 137 MET cc_start: -0.4829 (mtp) cc_final: -0.5610 (mmm) REVERT: C 231 LEU cc_start: 0.1652 (OUTLIER) cc_final: 0.1220 (pp) REVERT: C 235 LEU cc_start: 0.7620 (mt) cc_final: 0.7355 (mm) REVERT: C 287 LEU cc_start: 0.0616 (OUTLIER) cc_final: 0.0135 (tp) REVERT: D 72 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.6352 (t) REVERT: D 110 MET cc_start: 0.5424 (mtt) cc_final: 0.5004 (tmm) REVERT: D 137 MET cc_start: -0.6252 (ptp) cc_final: -0.6585 (mmt) REVERT: D 185 MET cc_start: 0.6686 (mmm) cc_final: 0.5979 (mmm) outliers start: 48 outliers final: 31 residues processed: 423 average time/residue: 0.1240 time to fit residues: 79.4131 Evaluate side-chains 409 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 371 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 4 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN B 25 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.171361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104826 restraints weight = 29797.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108363 restraints weight = 13966.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110496 restraints weight = 8490.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111963 restraints weight = 6024.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112893 restraints weight = 4736.526| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16299 Z= 0.131 Angle : 0.584 15.737 22004 Z= 0.304 Chirality : 0.041 0.185 2348 Planarity : 0.003 0.054 2812 Dihedral : 6.933 54.481 2268 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.57 % Allowed : 20.19 % Favored : 77.25 % 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: 1.56 (0.19), residues: 1928 helix: 1.64 (0.15), residues: 1131 sheet: -0.39 (0.40), residues: 144 loop : 0.48 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 274 TYR 0.015 0.001 TYR C 22 PHE 0.018 0.001 PHE A 261 TRP 0.029 0.002 TRP D 124 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16298) covalent geometry : angle 0.58371 / 0.30 (22004) hydrogen bonds : bond 0.03675 / 2.34 ( 896) hydrogen bonds : angle 4.77170 / 3.33 ( 2616) Misc. bond : bond 0.01009 / 0.53 ( 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 443 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 399 time to evaluate : 0.613 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 119 GLU cc_start: 0.8791 (mp0) cc_final: 0.8461 (mp0) REVERT: A 161 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7427 (mtm180) REVERT: A 173 LEU cc_start: 0.9635 (mt) cc_final: 0.9278 (mt) REVERT: A 178 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 232 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8842 (m-40) REVERT: A 250 TYR cc_start: 0.8847 (m-80) cc_final: 0.8268 (m-80) REVERT: A 274 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7720 (tpp-160) REVERT: A 379 SER cc_start: 0.9103 (t) cc_final: 0.8446 (t) REVERT: A 384 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.6657 (pm20) REVERT: A 406 ASP cc_start: 0.8089 (m-30) cc_final: 0.7844 (t0) REVERT: A 446 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7567 (mmm160) REVERT: A 466 MET cc_start: 0.9205 (ptm) cc_final: 0.8951 (ptp) REVERT: A 493 MET cc_start: 0.9287 (tmm) cc_final: 0.8598 (tmm) REVERT: A 586 TYR cc_start: 0.8819 (m-10) cc_final: 0.8549 (m-10) REVERT: B 135 GLU cc_start: 0.8261 (mp0) cc_final: 0.7917 (mp0) REVERT: B 483 GLU cc_start: 0.8725 (mp0) cc_final: 0.8308 (pm20) REVERT: B 526 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7336 (tp30) REVERT: B 590 SER cc_start: 0.9538 (t) cc_final: 0.8832 (p) REVERT: B 640 MET cc_start: 0.8991 (tpp) cc_final: 0.8550 (tpp) REVERT: B 668 ASN cc_start: 0.9029 (m-40) cc_final: 0.8821 (m-40) REVERT: C 129 LYS cc_start: 0.7673 (tptp) cc_final: 0.6668 (ptmt) REVERT: C 287 LEU cc_start: 0.0708 (OUTLIER) cc_final: 0.0190 (tp) REVERT: D 110 MET cc_start: 0.5402 (mtt) cc_final: 0.5021 (tmm) REVERT: D 137 MET cc_start: -0.5790 (ptp) cc_final: -0.6626 (mmt) outliers start: 44 outliers final: 29 residues processed: 425 average time/residue: 0.1232 time to fit residues: 79.6013 Evaluate side-chains 408 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 374 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU 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 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103985 restraints weight = 29809.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108927 restraints weight = 15344.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109453 restraints weight = 8842.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110671 restraints weight = 6698.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112957 restraints weight = 5066.447| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16299 Z= 0.188 Angle : 0.603 10.992 22004 Z= 0.318 Chirality : 0.043 0.197 2348 Planarity : 0.004 0.051 2812 Dihedral : 6.887 54.907 2268 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.09 % Allowed : 19.95 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.19), residues: 1928 helix: 1.64 (0.15), residues: 1121 sheet: -0.45 (0.40), residues: 144 loop : 0.39 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.020 0.001 TYR D 142 PHE 0.019 0.001 PHE C 21 TRP 0.021 0.002 TRP D 124 HIS 0.015 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (16298) covalent geometry : angle 0.60328 / 0.32 (22004) hydrogen bonds : bond 0.03790 / 2.41 ( 896) hydrogen bonds : angle 4.82337 / 3.37 ( 2616) Misc. bond : bond 0.00681 / 0.36 ( 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 429 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 376 time to evaluate : 0.612 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: A 31 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: A 119 GLU cc_start: 0.8838 (mp0) cc_final: 0.8478 (mp0) REVERT: A 178 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 250 TYR cc_start: 0.8868 (m-80) cc_final: 0.8209 (m-80) REVERT: A 274 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7774 (tpp-160) REVERT: A 379 SER cc_start: 0.9015 (t) cc_final: 0.8351 (t) REVERT: A 384 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: A 493 MET cc_start: 0.9270 (tmm) cc_final: 0.8523 (tmm) REVERT: A 586 TYR cc_start: 0.8847 (m-10) cc_final: 0.8604 (m-10) REVERT: B 104 TYR cc_start: 0.9001 (m-80) cc_final: 0.8233 (m-80) REVERT: B 135 GLU cc_start: 0.8229 (mp0) cc_final: 0.7948 (mp0) REVERT: B 317 MET cc_start: 0.8601 (mtt) cc_final: 0.8353 (mtt) REVERT: B 406 ASP cc_start: 0.8001 (m-30) cc_final: 0.7571 (t0) REVERT: B 526 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7362 (tp30) REVERT: B 590 SER cc_start: 0.9536 (t) cc_final: 0.8811 (p) REVERT: B 640 MET cc_start: 0.8993 (tpp) cc_final: 0.8550 (tpp) REVERT: B 668 ASN cc_start: 0.9049 (m-40) cc_final: 0.8802 (m-40) REVERT: C 129 LYS cc_start: 0.7654 (tptp) cc_final: 0.6624 (ptmt) REVERT: C 231 LEU cc_start: 0.1826 (OUTLIER) cc_final: 0.1348 (pp) REVERT: C 287 LEU cc_start: 0.0559 (OUTLIER) cc_final: 0.0159 (tp) REVERT: D 110 MET cc_start: 0.5289 (mtt) cc_final: 0.4919 (tmm) REVERT: D 137 MET cc_start: -0.5880 (ptp) cc_final: -0.6775 (mmt) outliers start: 53 outliers final: 38 residues processed: 407 average time/residue: 0.1138 time to fit residues: 70.3098 Evaluate side-chains 404 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3976 r_free = 0.3976 target = 0.167085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101876 restraints weight = 30147.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105239 restraints weight = 14382.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107360 restraints weight = 8793.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108746 restraints weight = 6276.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109588 restraints weight = 4929.646| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16299 Z= 0.209 Angle : 0.637 13.718 22004 Z= 0.335 Chirality : 0.044 0.230 2348 Planarity : 0.004 0.048 2812 Dihedral : 7.047 56.073 2268 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.09 % Allowed : 20.48 % Favored : 76.43 % 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: 1.38 (0.19), residues: 1928 helix: 1.56 (0.15), residues: 1122 sheet: -0.39 (0.43), residues: 132 loop : 0.26 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.034 0.001 TYR C 204 PHE 0.019 0.001 PHE C 92 TRP 0.030 0.002 TRP D 124 HIS 0.010 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (16298) covalent geometry : angle 0.63682 / 0.33 (22004) hydrogen bonds : bond 0.03936 / 2.48 ( 896) hydrogen bonds : angle 4.89831 / 3.42 ( 2616) Misc. bond : bond 0.00531 / 0.28 ( 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 425 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: A 119 GLU cc_start: 0.8845 (mp0) cc_final: 0.8475 (mp0) REVERT: A 178 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8928 (p) REVERT: A 250 TYR cc_start: 0.8850 (m-80) cc_final: 0.8209 (m-80) REVERT: A 274 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7808 (tpp-160) REVERT: A 379 SER cc_start: 0.9024 (t) cc_final: 0.8426 (t) REVERT: A 384 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: A 406 ASP cc_start: 0.8062 (m-30) cc_final: 0.7759 (t0) REVERT: A 493 MET cc_start: 0.9274 (tmm) cc_final: 0.8518 (tmm) REVERT: A 586 TYR cc_start: 0.8835 (m-10) cc_final: 0.8557 (m-10) REVERT: B 104 TYR cc_start: 0.9003 (m-80) cc_final: 0.8287 (m-80) REVERT: B 150 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8742 (tp-100) REVERT: B 232 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8577 (m-40) REVERT: B 406 ASP cc_start: 0.7997 (m-30) cc_final: 0.7597 (t0) REVERT: B 483 GLU cc_start: 0.8830 (mp0) cc_final: 0.8587 (pm20) REVERT: B 526 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7451 (tp30) REVERT: B 588 GLN cc_start: 0.8743 (mt0) cc_final: 0.8199 (mt0) REVERT: B 590 SER cc_start: 0.9485 (t) cc_final: 0.8782 (p) REVERT: C 129 LYS cc_start: 0.7657 (tptp) cc_final: 0.6626 (ptmt) REVERT: C 231 LEU cc_start: 0.1371 (OUTLIER) cc_final: 0.0892 (pp) REVERT: D 110 MET cc_start: 0.5358 (mtt) cc_final: 0.4950 (tmm) outliers start: 53 outliers final: 38 residues processed: 401 average time/residue: 0.1165 time to fit residues: 71.2997 Evaluate side-chains 403 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 GLN B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106314 restraints weight = 30072.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111426 restraints weight = 15124.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112241 restraints weight = 8225.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113902 restraints weight = 6284.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114184 restraints weight = 4776.497| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16299 Z= 0.147 Angle : 0.617 12.063 22004 Z= 0.324 Chirality : 0.043 0.283 2348 Planarity : 0.004 0.049 2812 Dihedral : 6.813 54.098 2265 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 21.59 % Favored : 76.25 % 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: 1.32 (0.19), residues: 1928 helix: 1.54 (0.15), residues: 1118 sheet: -0.49 (0.41), residues: 138 loop : 0.19 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 225 TYR 0.028 0.001 TYR C 204 PHE 0.017 0.001 PHE B 261 TRP 0.022 0.002 TRP C 44 HIS 0.009 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16298) covalent geometry : angle 0.61668 / 0.32 (22004) hydrogen bonds : bond 0.03825 / 2.41 ( 896) hydrogen bonds : angle 4.88914 / 3.42 ( 2616) Misc. bond : bond 0.00360 / 0.19 ( 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 417 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 380 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8128 (p0) cc_final: 0.7860 (p0) REVERT: A 30 LYS cc_start: 0.9363 (tppt) cc_final: 0.9049 (tppt) REVERT: A 119 GLU cc_start: 0.8754 (mp0) cc_final: 0.8408 (mp0) REVERT: A 161 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7367 (mtm180) REVERT: A 178 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8939 (p) REVERT: A 250 TYR cc_start: 0.8689 (m-80) cc_final: 0.8103 (m-80) REVERT: A 334 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8569 (ptpt) REVERT: A 379 SER cc_start: 0.9106 (t) cc_final: 0.8432 (t) REVERT: A 384 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: A 393 SER cc_start: 0.9043 (t) cc_final: 0.8557 (p) REVERT: A 433 THR cc_start: 0.9660 (m) cc_final: 0.9383 (p) REVERT: A 493 MET cc_start: 0.9255 (tmm) cc_final: 0.8577 (tmm) REVERT: A 586 TYR cc_start: 0.8768 (m-10) cc_final: 0.8545 (m-10) REVERT: B 104 TYR cc_start: 0.8949 (m-80) cc_final: 0.8212 (m-80) REVERT: B 232 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: B 406 ASP cc_start: 0.7947 (m-30) cc_final: 0.7543 (t0) REVERT: B 483 GLU cc_start: 0.8758 (mp0) cc_final: 0.8547 (pm20) REVERT: B 526 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7330 (tp30) REVERT: B 590 SER cc_start: 0.9449 (t) cc_final: 0.8638 (p) REVERT: B 640 MET cc_start: 0.8997 (tpp) cc_final: 0.8539 (tpp) REVERT: C 231 LEU cc_start: 0.1653 (OUTLIER) cc_final: 0.1222 (pp) REVERT: D 74 MET cc_start: 0.3451 (tpp) cc_final: 0.3045 (tpt) REVERT: D 110 MET cc_start: 0.5258 (mtt) cc_final: 0.4919 (tmm) outliers start: 37 outliers final: 27 residues processed: 401 average time/residue: 0.1212 time to fit residues: 73.7995 Evaluate side-chains 394 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107368 restraints weight = 30004.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112279 restraints weight = 15017.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112912 restraints weight = 8503.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114229 restraints weight = 6572.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115820 restraints weight = 4884.332| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16299 Z= 0.145 Angle : 0.653 18.229 22004 Z= 0.338 Chirality : 0.043 0.323 2348 Planarity : 0.004 0.053 2812 Dihedral : 6.759 54.621 2265 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 22.00 % Favored : 76.02 % 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: 1.24 (0.19), residues: 1928 helix: 1.46 (0.15), residues: 1127 sheet: -0.59 (0.41), residues: 138 loop : 0.18 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 225 TYR 0.029 0.001 TYR C 204 PHE 0.020 0.001 PHE C 92 TRP 0.031 0.002 TRP C 44 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16298) covalent geometry : angle 0.65286 / 0.34 (22004) hydrogen bonds : bond 0.03902 / 2.46 ( 896) hydrogen bonds : angle 4.88668 / 3.42 ( 2616) Misc. bond : bond 0.00269 / 0.14 ( 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 409 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 375 time to evaluate : 0.602 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 27 ASP cc_start: 0.8107 (p0) cc_final: 0.7837 (p0) REVERT: A 30 LYS cc_start: 0.9360 (tppt) cc_final: 0.9036 (tppt) REVERT: A 119 GLU cc_start: 0.8756 (mp0) cc_final: 0.8397 (mp0) REVERT: A 178 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8847 (p) REVERT: A 231 ASP cc_start: 0.8381 (t0) cc_final: 0.7933 (t0) REVERT: A 250 TYR cc_start: 0.8676 (m-80) cc_final: 0.8099 (m-80) REVERT: A 334 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8521 (ptpt) REVERT: A 379 SER cc_start: 0.9111 (t) cc_final: 0.8407 (t) REVERT: A 384 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: A 433 THR cc_start: 0.9656 (m) cc_final: 0.9355 (p) REVERT: A 493 MET cc_start: 0.9247 (tmm) cc_final: 0.8529 (tmm) REVERT: A 586 TYR cc_start: 0.8745 (m-10) cc_final: 0.8524 (m-10) REVERT: B 104 TYR cc_start: 0.8989 (m-80) cc_final: 0.8278 (m-80) REVERT: B 232 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8663 (m-40) REVERT: B 317 MET cc_start: 0.8654 (mtt) cc_final: 0.8233 (mtt) REVERT: B 406 ASP cc_start: 0.7955 (m-30) cc_final: 0.7555 (t0) REVERT: B 590 SER cc_start: 0.9411 (t) cc_final: 0.8550 (p) REVERT: B 640 MET cc_start: 0.8941 (tpp) cc_final: 0.8479 (tpp) REVERT: C 231 LEU cc_start: 0.1655 (OUTLIER) cc_final: 0.1254 (pp) REVERT: D 110 MET cc_start: 0.5237 (mtt) cc_final: 0.4860 (tmm) outliers start: 34 outliers final: 25 residues processed: 395 average time/residue: 0.1113 time to fit residues: 67.0004 Evaluate side-chains 385 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 355 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106596 restraints weight = 30287.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111418 restraints weight = 15490.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112246 restraints weight = 8865.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114062 restraints weight = 6685.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115183 restraints weight = 4735.224| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16299 Z= 0.148 Angle : 0.671 22.531 22004 Z= 0.343 Chirality : 0.043 0.313 2348 Planarity : 0.004 0.045 2812 Dihedral : 6.696 56.092 2265 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.16 % Allowed : 21.94 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1928 helix: 1.40 (0.15), residues: 1137 sheet: -0.61 (0.41), residues: 138 loop : 0.13 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 225 TYR 0.031 0.001 TYR C 204 PHE 0.024 0.001 PHE B 657 TRP 0.023 0.002 TRP C 44 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16298) covalent geometry : angle 0.67130 / 0.34 (22004) hydrogen bonds : bond 0.03856 / 2.43 ( 896) hydrogen bonds : angle 4.87218 / 3.41 ( 2616) Misc. bond : bond 0.00255 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.04 seconds wall clock time: 58 minutes 49.66 seconds (3529.66 seconds total)