Starting phenix.real_space_refine on Thu Aug 6 14:51:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwx_44985/08_2026/9bwx_44985_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwx_44985/08_2026/9bwx_44985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2026/9bwx_44985_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2026/9bwx_44985_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2026/9bwx_44985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2026/9bwx_44985.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.63, per 1000 atoms: 0.23 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 134.904, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 694.0 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A 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: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A 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: 3.547A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.722A 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: 5.842A 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: 4.173A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.565A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.313A 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: 4.314A 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: 5.889A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4956 1.34 - 1.46: 2920 1.46 - 1.58: 8247 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 4.92e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.85e+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 2.37e+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 1.16e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 21464 2.11 - 4.21: 467 4.21 - 6.32: 58 6.32 - 8.43: 8 8.43 - 10.53: 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 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.70 10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.80 -4.30 1.23e+00 6.61e-01 1.22e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8645 17.66 - 35.32: 853 35.32 - 52.98: 254 52.98 - 70.64: 64 70.64 - 88.29: 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 -134.29 12.29 0 2.50e+00 1.60e-01 2.42e+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 123.40 135.51 -12.11 0 2.50e+00 1.60e-01 2.35e+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 -134.31 11.71 0 2.50e+00 1.60e-01 2.19e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2122 0.093 - 0.187: 187 0.187 - 0.280: 34 0.280 - 0.374: 3 0.374 - 0.467: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+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 4.67e+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 3.00e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11880 3.11 - 3.70: 26437 3.70 - 4.30: 41184 4.30 - 4.90: 64920 Nonbonded interactions: 144552 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144547 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 individual isotropic 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.680 Find NCS groups from input model: 0.280 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 10.535 22004 Z= 0.462 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.909 88.295 6168 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.33 (16298) covalent geometry : angle 0.75591 / 0.46 (22004) hydrogen bonds : bond 0.16170 / 10.53 ( 896) hydrogen bonds : angle 6.35243 / 4.48 ( 2616) Misc. bond : bond 0.83345 / 43.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 411 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8416 (tpp-160) REVERT: B 274 ARG cc_start: 0.8031 (ptm160) cc_final: 0.7762 (ptp-110) outliers start: 23 outliers final: 6 residues processed: 427 average time/residue: 0.6973 time to fit residues: 326.4131 Evaluate side-chains 286 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 280 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 127 GLN 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: 0.0040 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 232 ASN A 668 ASN B 11 GLN B 14 ASN B 191 GLN B 418 ASN D 80 HIS D 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096336 restraints weight = 20769.881| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.41 r_work: 0.2837 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16299 Z= 0.172 Angle : 0.573 11.312 22004 Z= 0.309 Chirality : 0.042 0.191 2348 Planarity : 0.004 0.053 2812 Dihedral : 6.905 63.277 2276 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.86 % Allowed : 16.63 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 1928 helix: 1.75 (0.15), residues: 1125 sheet: 0.62 (0.42), residues: 126 loop : 0.63 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 446 TYR 0.019 0.001 TYR D 105 PHE 0.021 0.001 PHE B 624 TRP 0.012 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16298) covalent geometry : angle 0.57279 / 0.31 (22004) hydrogen bonds : bond 0.04377 / 2.77 ( 896) hydrogen bonds : angle 4.93012 / 3.46 ( 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 366 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 184 ARG cc_start: 0.9145 (tpp-160) cc_final: 0.8798 (tpp-160) REVERT: A 194 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8985 (tttm) REVERT: A 232 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8567 (m-40) REVERT: A 246 SER cc_start: 0.8138 (m) cc_final: 0.7642 (p) REVERT: A 274 ARG cc_start: 0.8547 (ttt90) cc_final: 0.8262 (ttt90) REVERT: A 276 LYS cc_start: 0.9211 (mtpp) cc_final: 0.8949 (mmpt) REVERT: A 296 LYS cc_start: 0.8733 (mttt) cc_final: 0.8172 (mmmt) REVERT: A 570 MET cc_start: 0.9511 (mtp) cc_final: 0.9293 (ttm) REVERT: A 602 GLU cc_start: 0.8962 (tt0) cc_final: 0.8282 (tt0) REVERT: A 604 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8523 (mmt90) REVERT: B 11 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 15 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 52 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9142 (tptm) REVERT: B 56 ASP cc_start: 0.9171 (m-30) cc_final: 0.8876 (m-30) REVERT: B 112 LYS cc_start: 0.9319 (mtpp) cc_final: 0.9093 (mtmm) REVERT: B 120 ASP cc_start: 0.8966 (m-30) cc_final: 0.8694 (m-30) REVERT: B 274 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7048 (ptp90) REVERT: B 276 LYS cc_start: 0.8994 (ptpp) cc_final: 0.8727 (mmtm) REVERT: B 341 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8997 (mmmm) REVERT: B 343 LEU cc_start: 0.9364 (mt) cc_final: 0.9119 (mt) REVERT: B 362 ASP cc_start: 0.8698 (m-30) cc_final: 0.8350 (m-30) REVERT: B 402 GLU cc_start: 0.8969 (tp30) cc_final: 0.8670 (mp0) REVERT: B 603 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 604 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8911 (mmp80) REVERT: B 610 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8439 (mtpp) REVERT: B 659 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8269 (mtpp) REVERT: C 56 MET cc_start: -0.0631 (mmp) cc_final: -0.1096 (tpt) REVERT: C 287 LEU cc_start: 0.0160 (OUTLIER) cc_final: -0.0061 (pp) outliers start: 49 outliers final: 9 residues processed: 345 average time/residue: 0.6550 time to fit residues: 248.4334 Evaluate side-chains 284 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN A 668 ASN B 109 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.093118 restraints weight = 21301.131| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.37 r_work: 0.2777 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16299 Z= 0.268 Angle : 0.579 10.627 22004 Z= 0.310 Chirality : 0.043 0.187 2348 Planarity : 0.004 0.051 2812 Dihedral : 6.901 63.794 2267 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.56 % Allowed : 16.34 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 1928 helix: 1.65 (0.15), residues: 1135 sheet: 0.14 (0.41), residues: 132 loop : 0.67 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 446 TYR 0.018 0.001 TYR C 46 PHE 0.018 0.002 PHE B 261 TRP 0.011 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 (16298) covalent geometry : angle 0.57920 / 0.31 (22004) hydrogen bonds : bond 0.04175 / 2.66 ( 896) hydrogen bonds : angle 4.85492 / 3.40 ( 2616) Misc. bond : bond 0.00318 / 0.17 ( 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 316 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 0.463 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 79 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 184 ARG cc_start: 0.9156 (tpp-160) cc_final: 0.8843 (tpp-160) REVERT: A 274 ARG cc_start: 0.8550 (ttt90) cc_final: 0.8164 (ttt90) REVERT: A 296 LYS cc_start: 0.8822 (mttt) cc_final: 0.8200 (mmmt) REVERT: A 316 GLU cc_start: 0.8591 (tp30) cc_final: 0.8350 (tp30) REVERT: A 444 ASP cc_start: 0.8678 (t70) cc_final: 0.8216 (p0) REVERT: A 446 ARG cc_start: 0.7308 (mmp-170) cc_final: 0.7082 (mmp-170) REVERT: A 570 MET cc_start: 0.9559 (mtp) cc_final: 0.9346 (ttm) REVERT: A 602 GLU cc_start: 0.8962 (tt0) cc_final: 0.8301 (tt0) REVERT: A 604 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8181 (mmt-90) REVERT: B 15 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8490 (mp0) REVERT: B 52 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9090 (tptm) REVERT: B 56 ASP cc_start: 0.9139 (m-30) cc_final: 0.8829 (m-30) REVERT: B 112 LYS cc_start: 0.9394 (mtpp) cc_final: 0.9036 (mtmm) REVERT: B 274 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7286 (ptp90) REVERT: B 341 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8978 (mmmm) REVERT: B 343 LEU cc_start: 0.9389 (mt) cc_final: 0.9144 (mt) REVERT: B 603 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 604 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8919 (mmp80) REVERT: B 610 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8559 (mtpp) REVERT: B 659 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8180 (mtpp) REVERT: B 686 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8176 (mtp85) REVERT: D 103 LYS cc_start: 0.5275 (tptm) cc_final: 0.4922 (pptt) outliers start: 61 outliers final: 22 residues processed: 287 average time/residue: 0.6480 time to fit residues: 203.6415 Evaluate side-chains 272 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 50.0000 chunk 132 optimal weight: 0.6980 chunk 185 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 171 optimal weight: 50.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 668 ASN B 11 GLN B 232 ASN D 24 GLN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093526 restraints weight = 21012.150| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.38 r_work: 0.2801 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16299 Z= 0.202 Angle : 0.544 10.980 22004 Z= 0.291 Chirality : 0.041 0.160 2348 Planarity : 0.003 0.047 2812 Dihedral : 6.840 61.335 2267 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.15 % Allowed : 17.09 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1928 helix: 1.65 (0.15), residues: 1136 sheet: -0.06 (0.42), residues: 132 loop : 0.63 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 446 TYR 0.025 0.001 TYR D 105 PHE 0.016 0.001 PHE B 100 TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (16298) covalent geometry : angle 0.54449 / 0.29 (22004) hydrogen bonds : bond 0.03793 / 2.41 ( 896) hydrogen bonds : angle 4.69452 / 3.29 ( 2616) Misc. bond : bond 0.00205 / 0.11 ( 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 310 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 184 ARG cc_start: 0.9210 (tpp-160) cc_final: 0.8857 (tpp-160) REVERT: A 274 ARG cc_start: 0.8638 (ttt90) cc_final: 0.8270 (ttt90) REVERT: A 276 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8785 (mmpt) REVERT: A 316 GLU cc_start: 0.8600 (tp30) cc_final: 0.8340 (tp30) REVERT: A 444 ASP cc_start: 0.8662 (t70) cc_final: 0.8054 (p0) REVERT: A 589 SER cc_start: 0.9603 (OUTLIER) cc_final: 0.9299 (t) REVERT: A 602 GLU cc_start: 0.8900 (tt0) cc_final: 0.8684 (tt0) REVERT: B 11 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: B 15 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8533 (mp0) REVERT: B 52 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9079 (tptm) REVERT: B 56 ASP cc_start: 0.9109 (m-30) cc_final: 0.8765 (m-30) REVERT: B 79 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 111 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8876 (mmtm) REVERT: B 120 ASP cc_start: 0.8963 (m-30) cc_final: 0.8726 (m-30) REVERT: B 194 LYS cc_start: 0.9210 (tttp) cc_final: 0.8972 (ptmt) REVERT: B 232 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8427 (m110) REVERT: B 274 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7341 (ptp90) REVERT: B 341 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9008 (mmmm) REVERT: B 343 LEU cc_start: 0.9405 (mt) cc_final: 0.9155 (mt) REVERT: B 402 GLU cc_start: 0.9001 (tp30) cc_final: 0.8750 (mp0) REVERT: B 603 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 604 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8783 (mmp80) REVERT: B 610 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8498 (mtpp) REVERT: B 659 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8240 (mtpp) REVERT: C 56 MET cc_start: -0.0527 (mmp) cc_final: -0.1042 (tpt) REVERT: D 103 LYS cc_start: 0.5199 (tptm) cc_final: 0.4829 (pptt) REVERT: D 269 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5710 (mpm) outliers start: 54 outliers final: 22 residues processed: 288 average time/residue: 0.6960 time to fit residues: 219.0971 Evaluate side-chains 280 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 164 optimal weight: 30.0000 chunk 189 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.093736 restraints weight = 21076.176| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.37 r_work: 0.2784 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16299 Z= 0.243 Angle : 0.563 11.715 22004 Z= 0.298 Chirality : 0.042 0.156 2348 Planarity : 0.003 0.047 2812 Dihedral : 6.931 60.989 2265 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.09 % Allowed : 17.62 % Favored : 79.29 % 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: 1.63 (0.19), residues: 1928 helix: 1.63 (0.15), residues: 1136 sheet: -0.30 (0.42), residues: 132 loop : 0.60 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 446 TYR 0.013 0.001 TYR C 46 PHE 0.017 0.001 PHE A 492 TRP 0.009 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (16298) covalent geometry : angle 0.56264 / 0.30 (22004) hydrogen bonds : bond 0.03812 / 2.43 ( 896) hydrogen bonds : angle 4.69197 / 3.28 ( 2616) Misc. bond : bond 0.00693 / 0.36 ( 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 309 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 112 LYS cc_start: 0.9351 (mtpp) cc_final: 0.8979 (ptpp) REVERT: A 184 ARG cc_start: 0.9150 (tpp-160) cc_final: 0.8808 (tpp-160) REVERT: A 274 ARG cc_start: 0.8612 (ttt90) cc_final: 0.8251 (ttt90) REVERT: A 276 LYS cc_start: 0.9139 (mtpp) cc_final: 0.8747 (mmpt) REVERT: A 316 GLU cc_start: 0.8596 (tp30) cc_final: 0.8338 (tp30) REVERT: A 444 ASP cc_start: 0.8675 (t70) cc_final: 0.8181 (p0) REVERT: A 446 ARG cc_start: 0.7391 (mmp-170) cc_final: 0.7138 (mmp-170) REVERT: A 589 SER cc_start: 0.9600 (OUTLIER) cc_final: 0.9312 (t) REVERT: A 604 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8223 (mmt-90) REVERT: B 11 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: B 15 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8561 (mp0) REVERT: B 52 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9054 (tptm) REVERT: B 56 ASP cc_start: 0.9087 (m-30) cc_final: 0.8758 (m-30) REVERT: B 60 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8675 (pp20) REVERT: B 79 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 120 ASP cc_start: 0.9025 (m-30) cc_final: 0.8757 (m-30) REVERT: B 232 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8411 (m110) REVERT: B 274 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7315 (ptp90) REVERT: B 335 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 341 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8990 (mmmm) REVERT: B 402 GLU cc_start: 0.9013 (tp30) cc_final: 0.8653 (mp0) REVERT: B 604 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8874 (mmp80) REVERT: B 659 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8242 (mtpp) REVERT: C 56 MET cc_start: -0.0639 (mmp) cc_final: -0.1131 (tpt) REVERT: D 103 LYS cc_start: 0.5308 (tptm) cc_final: 0.4983 (pptt) REVERT: D 269 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5863 (mpm) outliers start: 53 outliers final: 26 residues processed: 287 average time/residue: 0.6784 time to fit residues: 213.6788 Evaluate side-chains 275 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN B 62 GLN B 232 ASN C 192 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096364 restraints weight = 20868.661| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.32 r_work: 0.2835 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3483 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= 0.151 Angle : 0.540 12.033 22004 Z= 0.285 Chirality : 0.040 0.169 2348 Planarity : 0.003 0.050 2812 Dihedral : 6.640 59.506 2265 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.63 % Allowed : 18.96 % Favored : 78.41 % 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: 1.68 (0.19), residues: 1928 helix: 1.74 (0.15), residues: 1130 sheet: -0.42 (0.41), residues: 136 loop : 0.53 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 446 TYR 0.037 0.001 TYR D 105 PHE 0.016 0.001 PHE A 492 TRP 0.007 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16298) covalent geometry : angle 0.53966 / 0.28 (22004) hydrogen bonds : bond 0.03538 / 2.24 ( 896) hydrogen bonds : angle 4.58361 / 3.21 ( 2616) Misc. bond : bond 0.00544 / 0.29 ( 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 300 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 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: A 79 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 112 LYS cc_start: 0.9300 (mtpp) cc_final: 0.8966 (ptpp) REVERT: A 184 ARG cc_start: 0.9165 (tpp-160) cc_final: 0.8818 (tpp-160) REVERT: A 274 ARG cc_start: 0.8683 (ttt90) cc_final: 0.8059 (ttm170) REVERT: A 276 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8692 (mmtt) REVERT: A 296 LYS cc_start: 0.8808 (mttt) cc_final: 0.8184 (mmmt) REVERT: A 316 GLU cc_start: 0.8603 (tp30) cc_final: 0.8387 (tp30) REVERT: A 444 ASP cc_start: 0.8653 (t70) cc_final: 0.8076 (p0) REVERT: A 456 LYS cc_start: 0.9262 (mtpp) cc_final: 0.8822 (mtmp) REVERT: A 589 SER cc_start: 0.9633 (t) cc_final: 0.9347 (t) REVERT: A 602 GLU cc_start: 0.8867 (tt0) cc_final: 0.8475 (tt0) REVERT: B 11 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: B 15 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8504 (mp0) REVERT: B 52 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9116 (tptm) REVERT: B 56 ASP cc_start: 0.9051 (m-30) cc_final: 0.8750 (m-30) REVERT: B 79 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 112 LYS cc_start: 0.9314 (mtpp) cc_final: 0.9003 (mtmm) REVERT: B 120 ASP cc_start: 0.9010 (m-30) cc_final: 0.8752 (m-30) REVERT: B 170 CYS cc_start: 0.8593 (p) cc_final: 0.8259 (m) REVERT: B 194 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9081 (ptmt) REVERT: B 228 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8713 (mttt) REVERT: B 232 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8486 (m110) REVERT: B 246 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7704 (p) REVERT: B 274 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7127 (ptp90) REVERT: B 276 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8557 (mmtm) REVERT: B 335 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8258 (mt-10) REVERT: B 341 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8988 (mmmm) REVERT: B 343 LEU cc_start: 0.9363 (mt) cc_final: 0.9110 (mt) REVERT: B 362 ASP cc_start: 0.8720 (m-30) cc_final: 0.8346 (m-30) REVERT: B 402 GLU cc_start: 0.9027 (tp30) cc_final: 0.8736 (mp0) REVERT: B 604 ARG cc_start: 0.9286 (mmp80) cc_final: 0.8901 (mmp80) REVERT: B 610 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8641 (ttmm) REVERT: B 659 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8289 (mtpp) REVERT: B 686 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8230 (mtp85) REVERT: D 46 TYR cc_start: 0.8494 (m-10) cc_final: 0.8158 (p90) REVERT: D 269 MET cc_start: 0.6196 (mpp) cc_final: 0.5980 (mpm) outliers start: 45 outliers final: 19 residues processed: 279 average time/residue: 0.7136 time to fit residues: 217.9329 Evaluate side-chains 269 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS 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: 20.0000 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 147 optimal weight: 50.0000 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 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 = 0.4097 r_free = 0.4097 target = 0.182465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093479 restraints weight = 20820.117| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.35 r_work: 0.2803 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3552 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= 0.229 Angle : 0.587 13.079 22004 Z= 0.307 Chirality : 0.042 0.191 2348 Planarity : 0.004 0.057 2812 Dihedral : 6.557 60.577 2264 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.68 % Allowed : 19.37 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 1928 helix: 1.62 (0.15), residues: 1133 sheet: -0.44 (0.41), residues: 136 loop : 0.57 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 446 TYR 0.014 0.001 TYR D 213 PHE 0.020 0.001 PHE A 492 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (16298) covalent geometry : angle 0.58651 / 0.31 (22004) hydrogen bonds : bond 0.03670 / 2.34 ( 896) hydrogen bonds : angle 4.64151 / 3.25 ( 2616) Misc. bond : bond 0.00484 / 0.25 ( 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 291 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 0.638 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 79 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 112 LYS cc_start: 0.9331 (mtpp) cc_final: 0.8996 (ptpp) REVERT: A 184 ARG cc_start: 0.9163 (tpp-160) cc_final: 0.8807 (tpp-160) REVERT: A 274 ARG cc_start: 0.8714 (ttt90) cc_final: 0.8391 (ttm110) REVERT: A 276 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8676 (mmtt) REVERT: A 316 GLU cc_start: 0.8627 (tp30) cc_final: 0.8424 (tp30) REVERT: A 384 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: A 402 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8396 (mt-10) REVERT: A 444 ASP cc_start: 0.8579 (t70) cc_final: 0.8134 (p0) REVERT: A 589 SER cc_start: 0.9604 (t) cc_final: 0.9331 (t) REVERT: A 602 GLU cc_start: 0.8891 (tt0) cc_final: 0.8346 (tt0) REVERT: A 604 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8602 (mmt90) REVERT: B 11 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8442 (mt0) REVERT: B 15 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 52 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9118 (tptm) REVERT: B 56 ASP cc_start: 0.9064 (m-30) cc_final: 0.8764 (m-30) REVERT: B 79 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 112 LYS cc_start: 0.9333 (mtpp) cc_final: 0.9056 (mtpm) REVERT: B 194 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9018 (ptmt) REVERT: B 232 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8524 (m110) REVERT: B 274 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7305 (ptp90) REVERT: B 335 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 341 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8984 (mmmm) REVERT: B 343 LEU cc_start: 0.9364 (mt) cc_final: 0.9108 (mt) REVERT: B 526 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8374 (mp0) REVERT: B 603 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 604 ARG cc_start: 0.9300 (mmp80) cc_final: 0.8893 (mmp80) REVERT: B 659 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8271 (mtpp) REVERT: B 686 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8178 (mtp85) REVERT: D 46 TYR cc_start: 0.8490 (m-10) cc_final: 0.8139 (p90) REVERT: D 269 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5935 (mpm) outliers start: 46 outliers final: 22 residues processed: 270 average time/residue: 0.6345 time to fit residues: 188.2664 Evaluate side-chains 266 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 40.0000 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 167 optimal weight: 40.0000 chunk 154 optimal weight: 50.0000 chunk 174 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN C 216 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 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 = 0.4124 r_free = 0.4124 target = 0.184559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096633 restraints weight = 20912.307| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.39 r_work: 0.2832 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16299 Z= 0.161 Angle : 0.558 14.805 22004 Z= 0.293 Chirality : 0.041 0.185 2348 Planarity : 0.003 0.057 2812 Dihedral : 6.389 59.883 2264 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.45 % Allowed : 19.78 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 1928 helix: 1.66 (0.15), residues: 1131 sheet: -0.43 (0.42), residues: 136 loop : 0.54 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 446 TYR 0.033 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16298) covalent geometry : angle 0.55829 / 0.29 (22004) hydrogen bonds : bond 0.03522 / 2.24 ( 896) hydrogen bonds : angle 4.55969 / 3.19 ( 2616) Misc. bond : bond 0.00468 / 0.25 ( 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 293 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.640 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 79 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8183 (mm-30) REVERT: A 112 LYS cc_start: 0.9278 (mtpp) cc_final: 0.9039 (ptpp) REVERT: A 184 ARG cc_start: 0.9115 (tpp-160) cc_final: 0.8767 (tpp-160) REVERT: A 274 ARG cc_start: 0.8765 (ttt90) cc_final: 0.8484 (ttm110) REVERT: A 276 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8907 (mmpt) REVERT: A 296 LYS cc_start: 0.8799 (mttt) cc_final: 0.8169 (mmmt) REVERT: A 402 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8423 (mt-10) REVERT: A 444 ASP cc_start: 0.8602 (t70) cc_final: 0.8282 (t0) REVERT: A 446 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7529 (mmp-170) REVERT: A 589 SER cc_start: 0.9613 (t) cc_final: 0.9348 (t) REVERT: A 602 GLU cc_start: 0.8869 (tt0) cc_final: 0.8034 (tt0) REVERT: A 604 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8542 (mmt90) REVERT: B 11 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: B 15 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8551 (mm-30) REVERT: B 52 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9118 (tptm) REVERT: B 56 ASP cc_start: 0.9034 (m-30) cc_final: 0.8735 (m-30) REVERT: B 79 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 112 LYS cc_start: 0.9317 (mtpp) cc_final: 0.9020 (mtpm) REVERT: B 170 CYS cc_start: 0.8639 (p) cc_final: 0.8278 (m) REVERT: B 228 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8830 (mtmt) REVERT: B 232 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8520 (m110) REVERT: B 246 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7702 (p) REVERT: B 274 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7279 (ptp90) REVERT: B 335 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 341 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8958 (mmmm) REVERT: B 343 LEU cc_start: 0.9366 (mt) cc_final: 0.9090 (mt) REVERT: B 362 ASP cc_start: 0.8736 (m-30) cc_final: 0.8367 (m-30) REVERT: B 402 GLU cc_start: 0.8998 (tp30) cc_final: 0.8751 (mp0) REVERT: B 604 ARG cc_start: 0.9256 (mmp80) cc_final: 0.8752 (mmp80) REVERT: B 659 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8320 (mtpp) REVERT: B 686 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8250 (mtp85) REVERT: D 46 TYR cc_start: 0.8538 (m-10) cc_final: 0.8244 (p90) REVERT: D 74 MET cc_start: 0.3673 (ptp) cc_final: 0.3471 (ptm) REVERT: D 105 TYR cc_start: 0.2401 (OUTLIER) cc_final: 0.1776 (p90) REVERT: D 269 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5993 (mmp) outliers start: 42 outliers final: 25 residues processed: 275 average time/residue: 0.7103 time to fit residues: 213.8389 Evaluate side-chains 278 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 50.0000 chunk 28 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN B 191 GLN B 232 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 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 = 0.4101 r_free = 0.4101 target = 0.183006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094983 restraints weight = 20898.026| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.32 r_work: 0.2813 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16299 Z= 0.204 Angle : 0.595 17.177 22004 Z= 0.308 Chirality : 0.041 0.169 2348 Planarity : 0.003 0.061 2812 Dihedral : 6.410 60.530 2264 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.33 % Allowed : 20.65 % Favored : 77.01 % 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: 1.57 (0.19), residues: 1928 helix: 1.61 (0.15), residues: 1135 sheet: -0.48 (0.41), residues: 136 loop : 0.57 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 446 TYR 0.030 0.001 TYR D 105 PHE 0.020 0.001 PHE A 492 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (16298) covalent geometry : angle 0.59459 / 0.31 (22004) hydrogen bonds : bond 0.03610 / 2.30 ( 896) hydrogen bonds : angle 4.59161 / 3.21 ( 2616) Misc. bond : bond 0.00417 / 0.22 ( 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 287 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.622 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 30 LYS cc_start: 0.9241 (ttmm) cc_final: 0.8798 (tptt) REVERT: A 79 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 112 LYS cc_start: 0.9299 (mtpp) cc_final: 0.9009 (ptpp) REVERT: A 184 ARG cc_start: 0.9119 (tpp-160) cc_final: 0.8773 (tpp-160) REVERT: A 274 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8024 (ttm170) REVERT: A 276 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8709 (mmpt) REVERT: A 296 LYS cc_start: 0.8784 (mttt) cc_final: 0.8151 (mmmt) REVERT: A 384 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8656 (pp20) REVERT: A 402 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8382 (mt-10) REVERT: A 444 ASP cc_start: 0.8605 (t70) cc_final: 0.8250 (t0) REVERT: A 452 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8640 (ttm-80) REVERT: A 589 SER cc_start: 0.9609 (t) cc_final: 0.9340 (t) REVERT: A 602 GLU cc_start: 0.8872 (tt0) cc_final: 0.8053 (tt0) REVERT: A 604 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8545 (mmt90) REVERT: B 11 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8436 (mt0) REVERT: B 15 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8551 (mm-30) REVERT: B 52 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9111 (tptm) REVERT: B 56 ASP cc_start: 0.9038 (m-30) cc_final: 0.8740 (m-30) REVERT: B 79 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 111 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8739 (mmpt) REVERT: B 112 LYS cc_start: 0.9301 (mtpp) cc_final: 0.8999 (mtpm) REVERT: B 228 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8768 (mtmt) REVERT: B 232 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8568 (m110) REVERT: B 274 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7296 (ptp90) REVERT: B 335 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8164 (mt-10) REVERT: B 341 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8956 (mmmm) REVERT: B 343 LEU cc_start: 0.9363 (mt) cc_final: 0.9102 (mt) REVERT: B 396 ASP cc_start: 0.8896 (m-30) cc_final: 0.8654 (m-30) REVERT: B 402 GLU cc_start: 0.8994 (tp30) cc_final: 0.8709 (mp0) REVERT: B 526 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8444 (mp0) REVERT: B 604 ARG cc_start: 0.9128 (mmp80) cc_final: 0.8889 (mmp80) REVERT: B 659 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8304 (mtpp) REVERT: B 686 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8177 (mtp85) REVERT: C 56 MET cc_start: -0.1210 (tpp) cc_final: -0.1439 (tpt) REVERT: C 74 MET cc_start: 0.2102 (mpm) cc_final: 0.1706 (mmm) REVERT: C 319 ASP cc_start: 0.9224 (m-30) cc_final: 0.8953 (m-30) REVERT: D 105 TYR cc_start: 0.2328 (OUTLIER) cc_final: 0.1646 (p90) REVERT: D 269 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6121 (mmp) outliers start: 40 outliers final: 24 residues processed: 272 average time/residue: 0.6557 time to fit residues: 195.2975 Evaluate side-chains 280 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 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 = 0.4121 r_free = 0.4121 target = 0.184841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096988 restraints weight = 20929.502| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.37 r_work: 0.2855 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16299 Z= 0.143 Angle : 0.574 18.159 22004 Z= 0.300 Chirality : 0.040 0.182 2348 Planarity : 0.003 0.060 2812 Dihedral : 6.265 59.896 2264 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.98 % Allowed : 21.41 % Favored : 76.60 % 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: 1.63 (0.19), residues: 1928 helix: 1.66 (0.15), residues: 1135 sheet: -0.53 (0.40), residues: 144 loop : 0.63 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 446 TYR 0.027 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16298) covalent geometry : angle 0.57446 / 0.30 (22004) hydrogen bonds : bond 0.03409 / 2.17 ( 896) hydrogen bonds : angle 4.53742 / 3.18 ( 2616) Misc. bond : bond 0.00369 / 0.19 ( 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 297 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.444 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: 0.9240 (ttmm) cc_final: 0.8854 (tptt) REVERT: A 79 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 112 LYS cc_start: 0.9242 (mtpp) cc_final: 0.9003 (ptpp) REVERT: A 184 ARG cc_start: 0.9100 (tpp-160) cc_final: 0.8775 (tpp-160) REVERT: A 274 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8362 (ttm170) REVERT: A 276 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8717 (mmtt) REVERT: A 296 LYS cc_start: 0.8789 (mttt) cc_final: 0.8168 (mmmt) REVERT: A 384 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: A 402 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8299 (mp0) REVERT: A 444 ASP cc_start: 0.8578 (t70) cc_final: 0.8236 (t0) REVERT: A 446 ARG cc_start: 0.8434 (mmp-170) cc_final: 0.7877 (mmp-170) REVERT: A 589 SER cc_start: 0.9633 (t) cc_final: 0.9374 (t) REVERT: A 599 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8905 (mt-10) REVERT: A 602 GLU cc_start: 0.8842 (tt0) cc_final: 0.8047 (tt0) REVERT: A 604 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8523 (mmt90) REVERT: B 11 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: B 15 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 52 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9109 (tptm) REVERT: B 56 ASP cc_start: 0.9031 (m-30) cc_final: 0.8732 (m-30) REVERT: B 79 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 111 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8768 (mmpt) REVERT: B 112 LYS cc_start: 0.9269 (mtpp) cc_final: 0.8955 (mtpm) REVERT: B 170 CYS cc_start: 0.8585 (p) cc_final: 0.8275 (m) REVERT: B 228 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8855 (mtmt) REVERT: B 232 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8549 (m-40) REVERT: B 246 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7798 (p) REVERT: B 274 ARG cc_start: 0.8430 (ptm160) cc_final: 0.7242 (ptp90) REVERT: B 335 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8342 (mt-10) REVERT: B 341 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8949 (mmmm) REVERT: B 343 LEU cc_start: 0.9359 (mt) cc_final: 0.9102 (mt) REVERT: B 362 ASP cc_start: 0.8661 (m-30) cc_final: 0.8289 (m-30) REVERT: B 396 ASP cc_start: 0.8793 (m-30) cc_final: 0.8517 (m-30) REVERT: B 402 GLU cc_start: 0.9016 (tp30) cc_final: 0.8745 (mp0) REVERT: B 413 SER cc_start: 0.9492 (m) cc_final: 0.9270 (p) REVERT: B 526 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8431 (mp0) REVERT: B 659 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8296 (mtpp) REVERT: B 686 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8162 (mtp85) REVERT: C 56 MET cc_start: -0.1219 (tpp) cc_final: -0.1449 (tpt) REVERT: C 74 MET cc_start: 0.2197 (mpm) cc_final: 0.1847 (mmm) REVERT: C 317 ASP cc_start: 0.9145 (m-30) cc_final: 0.8432 (t0) REVERT: D 105 TYR cc_start: 0.2117 (OUTLIER) cc_final: 0.1345 (p90) REVERT: D 269 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6219 (mmp) outliers start: 34 outliers final: 23 residues processed: 282 average time/residue: 0.5837 time to fit residues: 180.5915 Evaluate side-chains 285 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 40.0000 chunk 162 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN A 668 ASN B 11 GLN B 131 ASN B 232 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098705 restraints weight = 20891.272| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.36 r_work: 0.2865 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16299 Z= 0.139 Angle : 0.585 18.170 22004 Z= 0.304 Chirality : 0.040 0.175 2348 Planarity : 0.003 0.057 2812 Dihedral : 6.199 60.091 2264 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.93 % Allowed : 21.65 % 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: 1.65 (0.19), residues: 1928 helix: 1.66 (0.15), residues: 1137 sheet: -0.43 (0.41), residues: 148 loop : 0.63 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 446 TYR 0.025 0.001 TYR D 105 PHE 0.030 0.001 PHE B 624 TRP 0.015 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16298) covalent geometry : angle 0.58506 / 0.30 (22004) hydrogen bonds : bond 0.03372 / 2.14 ( 896) hydrogen bonds : angle 4.50782 / 3.15 ( 2616) Misc. bond : bond 0.00336 / 0.18 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9050.90 seconds wall clock time: 154 minutes 22.32 seconds (9262.32 seconds total)