Starting phenix.real_space_refine on Fri Jul 3 19:24:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx9_45000/07_2026/9bx9_45000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx9_45000/07_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_45000/07_2026/9bx9_45000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx9_45000/07_2026/9bx9_45000.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx9_45000/07_2026/9bx9_45000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx9_45000/07_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.35, per 1000 atoms: 0.21 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: 1.29 Conformation dependent library (CDL) restraints added in 696.1 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: 0.42 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: 2.80 Time building geometry restraints manager: 1.71 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 3.060 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 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 ... (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: 1.110 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- 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 : 0.588 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: 0.1331 time to fit residues: 138.5561 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 : 0.558 ------------------------------------------------------------------------------- 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 646 GLN C 19 GLN C 28 GLN C 84 HIS C 91 ASN C 101 HIS C 201 HIS C 216 GLN D 71 ASN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100214 restraints weight = 29820.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103648 restraints weight = 14086.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105817 restraints weight = 8593.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107150 restraints weight = 6147.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108266 restraints weight = 4903.925| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 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: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3606 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= 0.264 Angle : 0.653 10.575 22004 Z= 0.356 Chirality : 0.044 0.191 2348 Planarity : 0.004 0.050 2812 Dihedral : 7.537 63.269 2280 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.62 % Allowed : 15.40 % Favored : 80.98 % 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: 1.72 (0.19), residues: 1928 helix: 1.61 (0.15), residues: 1127 sheet: 0.19 (0.40), residues: 140 loop : 0.73 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.023 0.002 TYR C 22 PHE 0.029 0.002 PHE A 261 TRP 0.019 0.003 TRP D 124 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 (16298) covalent geometry : angle 0.65298 / 0.36 (22004) hydrogen bonds : bond 0.04738 / 2.99 ( 896) hydrogen bonds : angle 5.05857 / 3.51 ( 2616) Misc. bond : bond 0.00044 / 0.02 ( 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 534 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 472 time to evaluate : 0.371 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 119 GLU cc_start: 0.8863 (mp0) cc_final: 0.8594 (mp0) REVERT: A 148 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 174 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 177 ASP cc_start: 0.8921 (t0) cc_final: 0.8607 (t0) REVERT: A 250 TYR cc_start: 0.8845 (m-80) cc_final: 0.8204 (m-80) REVERT: A 362 ASP cc_start: 0.7761 (m-30) cc_final: 0.7162 (m-30) REVERT: A 379 SER cc_start: 0.8844 (t) cc_final: 0.8166 (t) REVERT: A 406 ASP cc_start: 0.8237 (m-30) cc_final: 0.8028 (m-30) REVERT: A 493 MET cc_start: 0.9233 (tmm) cc_final: 0.8683 (tmm) REVERT: A 494 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8888 (mtp) REVERT: A 584 ILE cc_start: 0.9478 (tp) cc_final: 0.9249 (tp) REVERT: A 588 GLN cc_start: 0.9326 (mm-40) cc_final: 0.9116 (tp40) REVERT: A 686 ARG cc_start: 0.8066 (mmt-90) cc_final: 0.7717 (mtt90) REVERT: B 104 TYR cc_start: 0.8885 (m-80) cc_final: 0.8135 (m-80) REVERT: B 109 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8425 (m-40) REVERT: B 177 ASP cc_start: 0.8136 (t0) cc_final: 0.7769 (t0) REVERT: B 181 ASP cc_start: 0.8722 (m-30) cc_final: 0.8517 (m-30) REVERT: B 276 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8624 (mmtm) REVERT: B 286 ASP cc_start: 0.7852 (m-30) cc_final: 0.7563 (m-30) REVERT: B 290 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 334 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8964 (pttm) REVERT: B 362 ASP cc_start: 0.8433 (m-30) cc_final: 0.8098 (m-30) REVERT: B 586 TYR cc_start: 0.8769 (m-80) cc_final: 0.8502 (m-80) REVERT: B 612 TYR cc_start: 0.8475 (m-80) cc_final: 0.7809 (m-80) REVERT: B 640 MET cc_start: 0.9033 (tpp) cc_final: 0.8668 (tpp) REVERT: C 137 MET cc_start: -0.4910 (mtp) cc_final: -0.5368 (mmm) REVERT: C 205 VAL cc_start: 0.4072 (t) cc_final: 0.3635 (m) REVERT: C 287 LEU cc_start: 0.0102 (OUTLIER) cc_final: -0.0551 (tp) REVERT: D 110 MET cc_start: 0.5237 (mtt) cc_final: 0.4823 (tmm) REVERT: D 185 MET cc_start: 0.6178 (mmm) cc_final: 0.5833 (mmm) REVERT: D 282 ILE cc_start: 0.0122 (OUTLIER) cc_final: -0.0126 (mt) outliers start: 62 outliers final: 35 residues processed: 510 average time/residue: 0.1149 time to fit residues: 87.5652 Evaluate side-chains 421 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 380 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 267 ILE 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 334 LYS Chi-restraints excluded: chain B residue 349 LEU 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 Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 149 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 B 645 GLN B 646 GLN C 24 GLN C 25 ASN C 84 HIS D 28 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100683 restraints weight = 30134.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104173 restraints weight = 14012.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106281 restraints weight = 8494.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107705 restraints weight = 6017.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108652 restraints weight = 4740.880| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16299 Z= 0.169 Angle : 0.576 6.742 22004 Z= 0.311 Chirality : 0.042 0.159 2348 Planarity : 0.003 0.048 2812 Dihedral : 7.229 58.764 2275 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.15 % Allowed : 17.85 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 1928 helix: 1.63 (0.15), residues: 1132 sheet: 0.31 (0.40), residues: 134 loop : 0.59 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.020 0.001 TYR C 179 PHE 0.022 0.001 PHE A 261 TRP 0.026 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16298) covalent geometry : angle 0.57599 / 0.31 (22004) hydrogen bonds : bond 0.04223 / 2.68 ( 896) hydrogen bonds : angle 4.87432 / 3.38 ( 2616) Misc. bond : bond 0.00061 / 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 501 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 447 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9329 (tppt) cc_final: 0.8986 (tppt) REVERT: A 58 LEU cc_start: 0.9617 (mt) cc_final: 0.9406 (mt) REVERT: A 119 GLU cc_start: 0.8874 (mp0) cc_final: 0.8536 (mp0) REVERT: A 157 LEU cc_start: 0.9349 (tp) cc_final: 0.9108 (tp) REVERT: A 174 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 177 ASP cc_start: 0.8852 (t0) cc_final: 0.8498 (t0) REVERT: A 232 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8403 (m-40) REVERT: A 250 TYR cc_start: 0.8954 (m-80) cc_final: 0.8199 (m-80) REVERT: A 362 ASP cc_start: 0.7934 (m-30) cc_final: 0.7449 (m-30) REVERT: A 379 SER cc_start: 0.9000 (t) cc_final: 0.8331 (t) REVERT: A 406 ASP cc_start: 0.8116 (m-30) cc_final: 0.7810 (m-30) REVERT: A 433 THR cc_start: 0.9704 (m) cc_final: 0.9365 (p) REVERT: A 493 MET cc_start: 0.9260 (tmm) cc_final: 0.8595 (tmm) REVERT: A 686 ARG cc_start: 0.8133 (mmt-90) cc_final: 0.7842 (mtt90) REVERT: B 8 LYS cc_start: 0.8711 (tppt) cc_final: 0.8494 (tppt) REVERT: B 104 TYR cc_start: 0.8863 (m-80) cc_final: 0.7966 (m-80) REVERT: B 135 GLU cc_start: 0.8358 (mp0) cc_final: 0.8084 (mp0) REVERT: B 147 GLN cc_start: 0.9225 (mt0) cc_final: 0.8784 (mm-40) REVERT: B 274 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7081 (ttm-80) REVERT: B 286 ASP cc_start: 0.7863 (m-30) cc_final: 0.7644 (m-30) REVERT: B 334 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8909 (pttm) REVERT: B 362 ASP cc_start: 0.8394 (m-30) cc_final: 0.8017 (m-30) REVERT: B 526 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7522 (tp30) REVERT: B 586 TYR cc_start: 0.8670 (m-80) cc_final: 0.8278 (m-80) REVERT: B 634 MET cc_start: 0.9122 (mmm) cc_final: 0.8904 (mmt) REVERT: B 640 MET cc_start: 0.9025 (tpp) cc_final: 0.8593 (tpp) REVERT: C 137 MET cc_start: -0.4593 (mtp) cc_final: -0.5213 (mmm) REVERT: C 235 LEU cc_start: 0.7722 (mt) cc_final: 0.7418 (mm) REVERT: C 287 LEU cc_start: 0.0350 (OUTLIER) cc_final: -0.0040 (tp) REVERT: D 97 GLU cc_start: -0.1147 (OUTLIER) cc_final: -0.2789 (mt-10) REVERT: D 110 MET cc_start: 0.5370 (mtt) cc_final: 0.4996 (tmm) REVERT: D 137 MET cc_start: -0.6400 (ptp) cc_final: -0.7349 (tpp) REVERT: D 185 MET cc_start: 0.6483 (mmm) cc_final: 0.6153 (mmm) REVERT: D 282 ILE cc_start: 0.0587 (OUTLIER) cc_final: 0.0361 (mt) outliers start: 54 outliers final: 30 residues processed: 474 average time/residue: 0.1201 time to fit residues: 86.5614 Evaluate side-chains 420 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 384 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER 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 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 274 ARG 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 587 VAL Chi-restraints excluded: chain B residue 589 SER 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 C residue 316 LYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 0.0170 chunk 145 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 501 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.166202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100512 restraints weight = 30003.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103968 restraints weight = 14034.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106103 restraints weight = 8554.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107447 restraints weight = 6140.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108391 restraints weight = 4818.465| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16299 Z= 0.181 Angle : 0.571 9.248 22004 Z= 0.309 Chirality : 0.042 0.213 2348 Planarity : 0.003 0.050 2812 Dihedral : 7.160 55.369 2274 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.44 % Allowed : 18.90 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1928 helix: 1.59 (0.15), residues: 1133 sheet: -0.35 (0.39), residues: 152 loop : 0.66 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 274 TYR 0.036 0.001 TYR D 142 PHE 0.021 0.001 PHE A 261 TRP 0.026 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (16298) covalent geometry : angle 0.57051 / 0.31 (22004) hydrogen bonds : bond 0.04066 / 2.59 ( 896) hydrogen bonds : angle 4.84618 / 3.38 ( 2616) Misc. bond : bond 0.00172 / 0.09 ( 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 473 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9359 (tppt) cc_final: 0.8997 (tppt) REVERT: A 119 GLU cc_start: 0.8876 (mp0) cc_final: 0.8517 (mp0) REVERT: A 157 LEU cc_start: 0.9305 (tp) cc_final: 0.8872 (tp) REVERT: A 161 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7448 (mtm180) REVERT: A 178 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8802 (p) REVERT: A 250 TYR cc_start: 0.8947 (m-80) cc_final: 0.8241 (m-80) REVERT: A 334 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8577 (ptpt) REVERT: A 379 SER cc_start: 0.8987 (t) cc_final: 0.8421 (t) REVERT: A 384 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: A 406 ASP cc_start: 0.8037 (m-30) cc_final: 0.7702 (m-30) REVERT: A 657 PHE cc_start: 0.9024 (m-80) cc_final: 0.8798 (m-80) REVERT: A 686 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7721 (mtt90) REVERT: B 8 LYS cc_start: 0.8708 (tppt) cc_final: 0.8503 (tppt) REVERT: B 135 GLU cc_start: 0.8306 (mp0) cc_final: 0.7948 (mp0) REVERT: B 147 GLN cc_start: 0.9299 (mt0) cc_final: 0.8828 (mm-40) REVERT: B 232 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8635 (m-40) REVERT: B 286 ASP cc_start: 0.7879 (m-30) cc_final: 0.7674 (m-30) REVERT: B 334 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8945 (pttm) REVERT: B 348 MET cc_start: 0.8171 (tmm) cc_final: 0.7929 (tmm) REVERT: B 362 ASP cc_start: 0.8328 (m-30) cc_final: 0.8005 (m-30) REVERT: B 526 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7485 (tp30) REVERT: B 590 SER cc_start: 0.9559 (p) cc_final: 0.9287 (t) REVERT: B 640 MET cc_start: 0.9019 (tpp) cc_final: 0.8597 (tpp) REVERT: C 137 MET cc_start: -0.4758 (mtp) cc_final: -0.5380 (mmm) REVERT: C 197 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6093 (p0) REVERT: C 235 LEU cc_start: 0.7665 (mt) cc_final: 0.7343 (mm) REVERT: C 287 LEU cc_start: 0.0720 (OUTLIER) cc_final: 0.0167 (tp) REVERT: D 110 MET cc_start: 0.5541 (mtt) cc_final: 0.4951 (tmm) REVERT: D 137 MET cc_start: -0.6222 (ptp) cc_final: -0.6984 (tpp) REVERT: D 185 MET cc_start: 0.6543 (mmm) cc_final: 0.6214 (mmm) REVERT: D 282 ILE cc_start: 0.0935 (OUTLIER) cc_final: 0.0716 (mt) outliers start: 59 outliers final: 38 residues processed: 445 average time/residue: 0.1184 time to fit residues: 79.3233 Evaluate side-chains 418 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 372 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU 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 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR 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 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 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER 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 197 ASP 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 C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 282 ILE 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: 1.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 145 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100167 restraints weight = 30192.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103581 restraints weight = 14136.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105683 restraints weight = 8678.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107012 restraints weight = 6211.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107936 restraints weight = 4860.842| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16299 Z= 0.214 Angle : 0.587 8.517 22004 Z= 0.316 Chirality : 0.042 0.174 2348 Planarity : 0.004 0.048 2812 Dihedral : 7.258 53.978 2274 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.56 % Allowed : 19.78 % Favored : 76.66 % 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: 1.52 (0.19), residues: 1928 helix: 1.56 (0.15), residues: 1125 sheet: -0.12 (0.42), residues: 128 loop : 0.47 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.018 0.001 TYR D 142 PHE 0.018 0.002 PHE A 261 TRP 0.025 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (16298) covalent geometry : angle 0.58652 / 0.32 (22004) hydrogen bonds : bond 0.04078 / 2.59 ( 896) hydrogen bonds : angle 4.84831 / 3.38 ( 2616) Misc. bond : bond 0.00221 / 0.12 ( 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 448 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 387 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9373 (tppt) cc_final: 0.9009 (tppt) REVERT: A 119 GLU cc_start: 0.8841 (mp0) cc_final: 0.8457 (mp0) REVERT: A 250 TYR cc_start: 0.8922 (m-80) cc_final: 0.8202 (m-80) REVERT: A 274 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7666 (tpp-160) REVERT: A 334 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8644 (ptpt) REVERT: A 379 SER cc_start: 0.8993 (t) cc_final: 0.8320 (t) REVERT: A 384 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: A 406 ASP cc_start: 0.7990 (m-30) cc_final: 0.7711 (m-30) REVERT: A 686 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7710 (mtt90) REVERT: B 104 TYR cc_start: 0.8987 (m-80) cc_final: 0.8140 (m-80) REVERT: B 135 GLU cc_start: 0.8263 (mp0) cc_final: 0.7927 (mp0) REVERT: B 147 GLN cc_start: 0.9326 (mt0) cc_final: 0.8996 (mm-40) REVERT: B 148 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8618 (mt-10) REVERT: B 232 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8616 (m-40) REVERT: B 334 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8950 (pttm) REVERT: B 362 ASP cc_start: 0.8370 (m-30) cc_final: 0.7942 (m-30) REVERT: B 526 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7464 (tp30) REVERT: B 590 SER cc_start: 0.9634 (p) cc_final: 0.9292 (t) REVERT: B 640 MET cc_start: 0.8972 (tpp) cc_final: 0.8546 (tpp) REVERT: C 129 LYS cc_start: 0.7707 (tptp) cc_final: 0.6678 (ptmt) REVERT: C 197 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6319 (p0) REVERT: C 231 LEU cc_start: 0.1653 (OUTLIER) cc_final: 0.1104 (pp) REVERT: C 287 LEU cc_start: 0.0721 (OUTLIER) cc_final: 0.0149 (tp) REVERT: D 110 MET cc_start: 0.5496 (mtt) cc_final: 0.5063 (tmm) REVERT: D 137 MET cc_start: -0.6091 (ptp) cc_final: -0.6454 (mmt) REVERT: D 185 MET cc_start: 0.6505 (mmm) cc_final: 0.5798 (mmm) REVERT: D 205 VAL cc_start: 0.6246 (p) cc_final: 0.5960 (m) REVERT: D 282 ILE cc_start: 0.1509 (OUTLIER) cc_final: -0.0450 (mt) outliers start: 61 outliers final: 40 residues processed: 421 average time/residue: 0.1318 time to fit residues: 83.4625 Evaluate side-chains 412 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL 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 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 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 116 GLU Chi-restraints excluded: chain B residue 124 ILE 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 232 ASN Chi-restraints excluded: chain B residue 334 LYS 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 555 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 197 ASP 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 179 TYR Chi-restraints excluded: chain D residue 282 ILE 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: 6.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.169971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105435 restraints weight = 29641.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110531 restraints weight = 15142.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111110 restraints weight = 8239.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112393 restraints weight = 6495.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113311 restraints weight = 4833.505| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16299 Z= 0.126 Angle : 0.581 14.382 22004 Z= 0.305 Chirality : 0.041 0.182 2348 Planarity : 0.003 0.048 2812 Dihedral : 7.016 54.224 2274 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.68 % Allowed : 20.89 % 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: 1.48 (0.19), residues: 1928 helix: 1.57 (0.15), residues: 1127 sheet: -0.33 (0.40), residues: 140 loop : 0.42 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 274 TYR 0.018 0.001 TYR C 22 PHE 0.018 0.001 PHE A 261 TRP 0.025 0.001 TRP D 124 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (16298) covalent geometry : angle 0.58134 / 0.30 (22004) hydrogen bonds : bond 0.03840 / 2.40 ( 896) hydrogen bonds : angle 4.73436 / 3.30 ( 2616) Misc. bond : bond 0.00636 / 0.33 ( 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 465 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 419 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9355 (tppt) cc_final: 0.9046 (tppt) REVERT: A 119 GLU cc_start: 0.8733 (mp0) cc_final: 0.8388 (mp0) REVERT: A 173 LEU cc_start: 0.9645 (mt) cc_final: 0.9373 (mt) REVERT: A 178 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8959 (p) REVERT: A 250 TYR cc_start: 0.8805 (m-80) cc_final: 0.8246 (m-80) REVERT: A 274 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7694 (tpp-160) REVERT: A 334 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8573 (ptpt) REVERT: A 379 SER cc_start: 0.9140 (t) cc_final: 0.8408 (t) REVERT: A 406 ASP cc_start: 0.7928 (m-30) cc_final: 0.7673 (m-30) REVERT: A 433 THR cc_start: 0.9676 (m) cc_final: 0.9363 (p) REVERT: A 446 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7679 (mmm160) REVERT: A 586 TYR cc_start: 0.8807 (m-10) cc_final: 0.8549 (m-10) REVERT: A 640 MET cc_start: 0.9218 (tpp) cc_final: 0.8885 (tpp) REVERT: B 104 TYR cc_start: 0.8923 (m-80) cc_final: 0.8120 (m-80) REVERT: B 135 GLU cc_start: 0.8219 (mp0) cc_final: 0.7923 (mp0) REVERT: B 147 GLN cc_start: 0.9273 (mt0) cc_final: 0.8888 (mm-40) REVERT: B 232 ASN cc_start: 0.9128 (m-40) cc_final: 0.8633 (m-40) REVERT: B 274 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7345 (ttm-80) REVERT: B 317 MET cc_start: 0.8544 (mtt) cc_final: 0.8291 (mtt) REVERT: B 483 GLU cc_start: 0.8776 (mp0) cc_final: 0.8353 (pm20) REVERT: B 526 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7309 (tp30) REVERT: B 640 MET cc_start: 0.8945 (tpp) cc_final: 0.8484 (tpp) REVERT: C 23 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 129 LYS cc_start: 0.7673 (tptp) cc_final: 0.6682 (ptmt) REVERT: C 231 LEU cc_start: 0.1432 (OUTLIER) cc_final: 0.0927 (pp) REVERT: C 287 LEU cc_start: 0.0823 (OUTLIER) cc_final: 0.0373 (tp) REVERT: D 110 MET cc_start: 0.5471 (mtt) cc_final: 0.5117 (tmm) REVERT: D 137 MET cc_start: -0.5612 (ptp) cc_final: -0.6517 (mmt) REVERT: D 185 MET cc_start: 0.6071 (mmm) cc_final: 0.5755 (mmm) outliers start: 46 outliers final: 26 residues processed: 447 average time/residue: 0.1308 time to fit residues: 87.6826 Evaluate side-chains 411 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 379 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 435 SER 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 180 ASN Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 23 ASN 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 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 D residue 115 THR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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 = 0.3971 r_free = 0.3971 target = 0.166873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103881 restraints weight = 29665.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108939 restraints weight = 14841.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109708 restraints weight = 8072.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111305 restraints weight = 6094.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111682 restraints weight = 4540.216| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16299 Z= 0.197 Angle : 0.619 8.772 22004 Z= 0.325 Chirality : 0.043 0.191 2348 Planarity : 0.004 0.048 2812 Dihedral : 6.917 55.397 2268 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.80 % Allowed : 20.65 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.19), residues: 1928 helix: 1.57 (0.15), residues: 1128 sheet: -0.21 (0.42), residues: 128 loop : 0.46 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.026 0.001 TYR D 105 PHE 0.018 0.001 PHE A 492 TRP 0.016 0.002 TRP D 124 HIS 0.004 0.001 HIS B 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (16298) covalent geometry : angle 0.61890 / 0.32 (22004) hydrogen bonds : bond 0.03885 / 2.44 ( 896) hydrogen bonds : angle 4.82493 / 3.36 ( 2616) Misc. bond : bond 0.00638 / 0.34 ( 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 424 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 376 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8770 (mp0) cc_final: 0.8376 (mp0) REVERT: A 161 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7312 (mtm180) REVERT: A 178 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8965 (p) REVERT: A 250 TYR cc_start: 0.8875 (m-80) cc_final: 0.8300 (m-80) REVERT: A 334 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8589 (ptpt) REVERT: A 379 SER cc_start: 0.9043 (t) cc_final: 0.8419 (t) REVERT: A 384 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.6588 (pm20) REVERT: A 406 ASP cc_start: 0.7923 (m-30) cc_final: 0.7664 (m-30) REVERT: A 433 THR cc_start: 0.9676 (m) cc_final: 0.9384 (p) REVERT: A 586 TYR cc_start: 0.8839 (m-10) cc_final: 0.8562 (m-10) REVERT: B 104 TYR cc_start: 0.8985 (m-80) cc_final: 0.8239 (m-80) REVERT: B 135 GLU cc_start: 0.8242 (mp0) cc_final: 0.7977 (mp0) REVERT: B 147 GLN cc_start: 0.9300 (mt0) cc_final: 0.8913 (mm-40) REVERT: B 172 LEU cc_start: 0.9066 (mt) cc_final: 0.7891 (mt) REVERT: B 274 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7430 (ttm-80) REVERT: B 317 MET cc_start: 0.8587 (mtt) cc_final: 0.8359 (mtt) REVERT: B 406 ASP cc_start: 0.7964 (m-30) cc_final: 0.7552 (t0) REVERT: B 526 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7149 (tp30) REVERT: B 529 ASP cc_start: 0.7968 (m-30) cc_final: 0.6947 (m-30) REVERT: B 640 MET cc_start: 0.8917 (tpp) cc_final: 0.8499 (tpp) REVERT: C 23 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7635 (p0) REVERT: C 74 MET cc_start: 0.7801 (mpp) cc_final: 0.7503 (mpp) REVERT: C 231 LEU cc_start: 0.1403 (OUTLIER) cc_final: 0.0907 (pp) REVERT: C 287 LEU cc_start: 0.0617 (OUTLIER) cc_final: 0.0288 (tp) REVERT: D 110 MET cc_start: 0.5346 (mtt) cc_final: 0.4961 (tmm) REVERT: D 137 MET cc_start: -0.5838 (ptp) cc_final: -0.6659 (mmt) outliers start: 48 outliers final: 34 residues processed: 408 average time/residue: 0.1269 time to fit residues: 78.3005 Evaluate side-chains 403 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU 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 442 THR 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 124 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN 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 23 ASN 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 D residue 56 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 122 optimal weight: 0.0670 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104360 restraints weight = 30008.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108771 restraints weight = 14918.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109924 restraints weight = 7939.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111452 restraints weight = 6669.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111999 restraints weight = 4829.961| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16299 Z= 0.190 Angle : 0.642 15.503 22004 Z= 0.333 Chirality : 0.044 0.239 2348 Planarity : 0.004 0.048 2812 Dihedral : 7.005 59.454 2268 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.39 % Allowed : 21.59 % 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: 1.31 (0.19), residues: 1928 helix: 1.46 (0.15), residues: 1129 sheet: -0.67 (0.40), residues: 144 loop : 0.37 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 225 TYR 0.035 0.001 TYR C 204 PHE 0.020 0.001 PHE A 492 TRP 0.015 0.002 TRP D 124 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (16298) covalent geometry : angle 0.64231 / 0.33 (22004) hydrogen bonds : bond 0.03914 / 2.45 ( 896) hydrogen bonds : angle 4.88733 / 3.41 ( 2616) Misc. bond : bond 0.00675 / 0.36 ( 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 413 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 372 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8786 (mp0) cc_final: 0.8386 (mp0) REVERT: A 178 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8977 (p) REVERT: A 250 TYR cc_start: 0.8827 (m-80) cc_final: 0.8256 (m-80) REVERT: A 334 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8779 (pttm) REVERT: A 379 SER cc_start: 0.9061 (t) cc_final: 0.8428 (t) REVERT: A 433 THR cc_start: 0.9676 (m) cc_final: 0.9393 (p) REVERT: A 586 TYR cc_start: 0.8831 (m-10) cc_final: 0.8569 (m-10) REVERT: B 104 TYR cc_start: 0.9011 (m-80) cc_final: 0.8246 (m-80) REVERT: B 135 GLU cc_start: 0.8239 (mp0) cc_final: 0.8010 (mp0) REVERT: B 172 LEU cc_start: 0.9064 (mt) cc_final: 0.7884 (mt) REVERT: B 232 ASN cc_start: 0.8974 (t0) cc_final: 0.8730 (m-40) REVERT: B 274 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7563 (ttm-80) REVERT: B 406 ASP cc_start: 0.7994 (m-30) cc_final: 0.7601 (t0) REVERT: B 483 GLU cc_start: 0.8777 (mp0) cc_final: 0.8519 (mp0) REVERT: B 526 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7147 (tp30) REVERT: B 529 ASP cc_start: 0.7968 (m-30) cc_final: 0.6854 (m-30) REVERT: C 20 MET cc_start: 0.7364 (ppp) cc_final: 0.6812 (ppp) REVERT: C 23 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7764 (p0) REVERT: C 74 MET cc_start: 0.7540 (mpp) cc_final: 0.7181 (mpp) REVERT: C 197 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6506 (p0) REVERT: C 231 LEU cc_start: 0.1186 (OUTLIER) cc_final: 0.0699 (pp) REVERT: C 287 LEU cc_start: 0.0596 (OUTLIER) cc_final: 0.0309 (tp) REVERT: D 110 MET cc_start: 0.5380 (mtt) cc_final: 0.4986 (tmm) REVERT: D 137 MET cc_start: -0.5812 (ptp) cc_final: -0.6607 (mmt) outliers start: 41 outliers final: 30 residues processed: 399 average time/residue: 0.1265 time to fit residues: 77.2690 Evaluate side-chains 398 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 362 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 349 LEU Chi-restraints excluded: chain A residue 351 SER 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 124 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN 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 23 ASN 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 197 ASP 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 315 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 143 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS C 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.169965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106792 restraints weight = 30019.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111038 restraints weight = 14592.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112243 restraints weight = 8134.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113519 restraints weight = 6832.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114413 restraints weight = 5009.063| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16299 Z= 0.139 Angle : 0.627 17.704 22004 Z= 0.324 Chirality : 0.043 0.315 2348 Planarity : 0.003 0.046 2812 Dihedral : 6.862 53.942 2268 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.16 % Allowed : 22.00 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 1928 helix: 1.44 (0.15), residues: 1128 sheet: -0.47 (0.41), residues: 138 loop : 0.26 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 225 TYR 0.028 0.001 TYR C 204 PHE 0.022 0.001 PHE C 92 TRP 0.024 0.002 TRP C 44 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16298) covalent geometry : angle 0.62686 / 0.32 (22004) hydrogen bonds : bond 0.03879 / 2.42 ( 896) hydrogen bonds : angle 4.88928 / 3.42 ( 2616) Misc. bond : bond 0.00319 / 0.17 ( 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 433 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 396 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8696 (mp0) cc_final: 0.8313 (mp0) REVERT: A 178 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 231 ASP cc_start: 0.8437 (t0) cc_final: 0.8026 (t0) REVERT: A 250 TYR cc_start: 0.8678 (m-80) cc_final: 0.8096 (m-80) REVERT: A 334 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8613 (ptpt) REVERT: A 379 SER cc_start: 0.9150 (t) cc_final: 0.8417 (t) REVERT: A 384 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.6610 (pm20) REVERT: A 433 THR cc_start: 0.9646 (m) cc_final: 0.9373 (p) REVERT: A 586 TYR cc_start: 0.8759 (m-10) cc_final: 0.8527 (m-10) REVERT: B 104 TYR cc_start: 0.8960 (m-80) cc_final: 0.8194 (m-80) REVERT: B 147 GLN cc_start: 0.9288 (mt0) cc_final: 0.8794 (mm-40) REVERT: B 274 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7599 (ttm-80) REVERT: B 406 ASP cc_start: 0.7925 (m-30) cc_final: 0.7525 (t0) REVERT: B 529 ASP cc_start: 0.7969 (m-30) cc_final: 0.6807 (m-30) REVERT: B 588 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8705 (mm-40) REVERT: B 612 TYR cc_start: 0.8518 (m-80) cc_final: 0.8238 (m-80) REVERT: B 640 MET cc_start: 0.8996 (tpp) cc_final: 0.8573 (tpp) REVERT: C 20 MET cc_start: 0.7555 (ppp) cc_final: 0.7045 (ppp) REVERT: C 23 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7787 (p0) REVERT: C 74 MET cc_start: 0.7287 (mpp) cc_final: 0.6840 (mpp) REVERT: C 197 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6273 (p0) REVERT: C 231 LEU cc_start: 0.1377 (OUTLIER) cc_final: 0.0932 (pp) REVERT: D 110 MET cc_start: 0.5363 (mtt) cc_final: 0.4956 (tmm) REVERT: D 137 MET cc_start: -0.5863 (ptp) cc_final: -0.6627 (mmt) outliers start: 37 outliers final: 26 residues processed: 421 average time/residue: 0.1270 time to fit residues: 81.2567 Evaluate side-chains 400 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 368 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 349 LEU 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 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 197 ASP 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 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 243 THR 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: 5.9990 chunk 130 optimal weight: 0.7980 chunk 191 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN C 80 HIS D 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106667 restraints weight = 30130.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111277 restraints weight = 14947.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112208 restraints weight = 8370.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113959 restraints weight = 6286.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114797 restraints weight = 4501.063| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5786 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= 0.145 Angle : 0.661 20.720 22004 Z= 0.340 Chirality : 0.043 0.308 2348 Planarity : 0.004 0.043 2812 Dihedral : 6.748 55.009 2266 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.98 % Allowed : 22.05 % Favored : 75.96 % 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: 1.18 (0.19), residues: 1928 helix: 1.39 (0.15), residues: 1113 sheet: -0.49 (0.42), residues: 138 loop : 0.21 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 225 TYR 0.025 0.001 TYR D 105 PHE 0.025 0.001 PHE C 92 TRP 0.031 0.002 TRP C 44 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (16298) covalent geometry : angle 0.66095 / 0.34 (22004) hydrogen bonds : bond 0.03940 / 2.45 ( 896) hydrogen bonds : angle 4.93635 / 3.46 ( 2616) Misc. bond : bond 0.00253 / 0.13 ( 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 414 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 380 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8671 (mp0) cc_final: 0.8278 (mp0) REVERT: A 178 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 250 TYR cc_start: 0.8576 (m-80) cc_final: 0.7950 (m-80) REVERT: A 334 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8602 (ptpt) REVERT: A 379 SER cc_start: 0.9125 (t) cc_final: 0.8310 (t) REVERT: A 433 THR cc_start: 0.9632 (m) cc_final: 0.9395 (p) REVERT: B 17 MET cc_start: 0.8126 (mmm) cc_final: 0.7543 (mmm) REVERT: B 104 TYR cc_start: 0.8970 (m-80) cc_final: 0.8251 (m-80) REVERT: B 274 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7630 (ttm-80) REVERT: B 406 ASP cc_start: 0.7938 (m-30) cc_final: 0.7564 (t0) REVERT: B 640 MET cc_start: 0.8931 (tpp) cc_final: 0.8478 (tpp) REVERT: C 20 MET cc_start: 0.7514 (ppp) cc_final: 0.7055 (ppp) REVERT: C 23 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7872 (p0) REVERT: C 74 MET cc_start: 0.7369 (mpp) cc_final: 0.6945 (mpp) REVERT: C 204 TYR cc_start: 0.5430 (m-80) cc_final: 0.4850 (m-80) REVERT: C 231 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.0889 (pp) REVERT: D 110 MET cc_start: 0.5489 (mtt) cc_final: 0.5005 (tmm) REVERT: D 137 MET cc_start: -0.5853 (ptp) cc_final: -0.6667 (mmt) outliers start: 34 outliers final: 25 residues processed: 400 average time/residue: 0.1301 time to fit residues: 78.4967 Evaluate side-chains 397 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 368 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 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 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 B residue 599 GLU Chi-restraints excluded: chain C residue 23 ASN 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 231 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 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: 4.9990 chunk 123 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 chunk 162 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** D 201 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 = 0.3991 r_free = 0.3991 target = 0.168448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104921 restraints weight = 30039.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108317 restraints weight = 14065.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110373 restraints weight = 8494.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111783 restraints weight = 6046.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112687 restraints weight = 4706.432| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16299 Z= 0.178 Angle : 0.701 20.845 22004 Z= 0.354 Chirality : 0.045 0.306 2348 Planarity : 0.004 0.046 2812 Dihedral : 6.812 56.347 2266 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.87 % Allowed : 22.40 % Favored : 75.73 % 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: 1.11 (0.19), residues: 1928 helix: 1.33 (0.15), residues: 1115 sheet: -0.29 (0.45), residues: 126 loop : 0.12 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 225 TYR 0.029 0.001 TYR D 105 PHE 0.026 0.001 PHE C 92 TRP 0.026 0.002 TRP C 44 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (16298) covalent geometry : angle 0.70101 / 0.35 (22004) hydrogen bonds : bond 0.03948 / 2.49 ( 896) hydrogen bonds : angle 4.99691 / 3.50 ( 2616) Misc. bond : bond 0.00335 / 0.18 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.02 seconds wall clock time: 59 minutes 35.28 seconds (3575.28 seconds total)