Starting phenix.real_space_refine on Sat Jun 14 05:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx6_44995/06_2025/9bx6_44995_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx6_44995/06_2025/9bx6_44995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx6_44995/06_2025/9bx6_44995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx6_44995/06_2025/9bx6_44995.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx6_44995/06_2025/9bx6_44995_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx6_44995/06_2025/9bx6_44995_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.04, per 1000 atoms: 0.57 Number of scatterers: 15954 At special positions: 0 Unit cell: (94.024, 136.948, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.52 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: 4.058A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A 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: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A 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: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A 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: 7.140A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.737A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.314A 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: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.457A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A 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: 5.15 Time building geometry restraints manager: 4.55 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: 4936 1.34 - 1.46: 2932 1.46 - 1.58: 8255 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: 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 2.38e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.91e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.39e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.92e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21503 2.09 - 4.17: 464 4.17 - 6.26: 33 6.26 - 8.34: 2 8.34 - 10.43: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.51 3.68 1.06e+00 8.90e-01 1.21e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.15e+00 7.56e-01 1.20e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 9429 34.32 - 68.63: 329 68.63 - 102.95: 48 102.95 - 137.26: 0 137.26 - 171.58: 2 Dihedral angle restraints: 9808 sinusoidal: 4062 harmonic: 5746 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 130.11 171.58 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.71 165.97 1 2.00e+01 2.50e-03 4.73e+01 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 -134.30 12.30 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2127 0.093 - 0.185: 181 0.185 - 0.278: 32 0.278 - 0.371: 6 0.371 - 0.464: 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 2.05 0.46 2.00e-01 2.50e+01 5.37e+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 4.64e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+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 5.50e-02 4.84e+00 pdb=" N PRO B 7 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+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 2.15e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11864 3.11 - 3.70: 26421 3.70 - 4.30: 41219 4.30 - 4.90: 64952 Nonbonded interactions: 144588 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144583 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: 1.460 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: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.800 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.008 0.833 16299 Z= 0.724 Angle : 0.707 10.429 22004 Z= 0.453 Chirality : 0.059 0.464 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.576 6120 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE D 92 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.16166 ( 896) hydrogen bonds : angle 6.35133 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70747 (22004) Misc. bond : bond 0.83331 ( 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 789 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 765 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.6946 (m90) cc_final: 0.6571 (m90) REVERT: A 172 LEU cc_start: 0.9000 (mp) cc_final: 0.8767 (mp) REVERT: A 350 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7929 (mtp85) REVERT: A 584 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8403 (tp) REVERT: B 40 TYR cc_start: 0.8191 (t80) cc_final: 0.7944 (t80) REVERT: B 172 LEU cc_start: 0.9229 (mp) cc_final: 0.9015 (mp) REVERT: B 309 GLU cc_start: 0.7790 (tp30) cc_final: 0.7493 (tp30) REVERT: B 358 ILE cc_start: 0.9166 (mm) cc_final: 0.8946 (mm) REVERT: B 362 ASP cc_start: 0.7788 (m-30) cc_final: 0.7545 (m-30) REVERT: B 375 LYS cc_start: 0.8497 (mptp) cc_final: 0.8283 (mmtt) REVERT: C 47 LEU cc_start: 0.1019 (mt) cc_final: 0.0746 (mt) REVERT: C 213 TYR cc_start: 0.0977 (t80) cc_final: 0.0440 (t80) REVERT: C 286 VAL cc_start: 0.4277 (t) cc_final: 0.3512 (p) outliers start: 24 outliers final: 6 residues processed: 771 average time/residue: 0.3112 time to fit residues: 344.3966 Evaluate side-chains 483 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 476 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 14 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 668 ASN B 14 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 181 GLN C 249 GLN D 186 GLN D 238 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.092229 restraints weight = 25448.979| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.87 r_work: 0.2712 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 16299 Z= 0.325 Angle : 0.716 12.992 22004 Z= 0.377 Chirality : 0.047 0.359 2348 Planarity : 0.004 0.051 2812 Dihedral : 9.528 167.810 2228 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.68 % Allowed : 17.09 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1928 helix: 1.44 (0.15), residues: 1121 sheet: 0.11 (0.39), residues: 148 loop : 0.73 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 124 HIS 0.008 0.001 HIS C 201 PHE 0.035 0.003 PHE A 100 TYR 0.025 0.002 TYR C 173 ARG 0.007 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 896) hydrogen bonds : angle 5.26642 ( 2616) covalent geometry : bond 0.00732 (16298) covalent geometry : angle 0.71567 (22004) Misc. bond : bond 0.00203 ( 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 579 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 516 time to evaluate : 1.883 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 49 HIS cc_start: 0.8716 (m90) cc_final: 0.8164 (m90) REVERT: A 67 GLU cc_start: 0.8818 (mp0) cc_final: 0.8378 (mp0) REVERT: A 209 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8943 (ttmm) REVERT: A 266 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8741 (mtmm) REVERT: A 274 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8149 (ttm-80) REVERT: A 336 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9245 (ttmm) REVERT: A 383 SER cc_start: 0.9467 (m) cc_final: 0.9223 (t) REVERT: A 394 TYR cc_start: 0.9406 (m-80) cc_final: 0.9064 (m-80) REVERT: A 444 ASP cc_start: 0.8122 (t70) cc_final: 0.7884 (t70) REVERT: A 548 GLU cc_start: 0.8768 (tp30) cc_final: 0.8455 (tp30) REVERT: A 598 MET cc_start: 0.9066 (ttm) cc_final: 0.8682 (mtt) REVERT: A 628 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8663 (mt-10) REVERT: B 31 GLU cc_start: 0.8842 (mp0) cc_final: 0.8331 (pm20) REVERT: B 56 ASP cc_start: 0.9032 (m-30) cc_final: 0.8635 (m-30) REVERT: B 64 TYR cc_start: 0.9251 (m-10) cc_final: 0.8746 (m-10) REVERT: B 109 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: B 148 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 274 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7295 (ptp-170) REVERT: B 276 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8660 (mmtm) REVERT: B 474 GLN cc_start: 0.9289 (mt0) cc_final: 0.9075 (mt0) REVERT: B 493 MET cc_start: 0.9573 (tmm) cc_final: 0.9301 (tmm) REVERT: B 586 TYR cc_start: 0.9391 (m-80) cc_final: 0.9055 (m-80) REVERT: B 588 GLN cc_start: 0.9467 (mm110) cc_final: 0.9132 (mm-40) REVERT: B 628 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 681 THR cc_start: 0.9442 (p) cc_final: 0.9143 (p) REVERT: B 686 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8135 (ttm-80) REVERT: C 47 LEU cc_start: 0.5365 (mt) cc_final: 0.4985 (mt) REVERT: C 177 TYR cc_start: 0.9179 (t80) cc_final: 0.8977 (t80) REVERT: C 178 PHE cc_start: 0.7901 (m-80) cc_final: 0.7625 (m-80) REVERT: C 184 LEU cc_start: 0.4945 (mt) cc_final: 0.4606 (mp) REVERT: C 193 LEU cc_start: 0.7931 (mt) cc_final: 0.7586 (tt) REVERT: C 236 TYR cc_start: 0.8456 (t80) cc_final: 0.8212 (t80) REVERT: C 268 LEU cc_start: 0.7335 (mt) cc_final: 0.6997 (tp) REVERT: C 273 PHE cc_start: 0.5909 (m-80) cc_final: 0.3530 (t80) REVERT: C 282 ILE cc_start: 0.3855 (tt) cc_final: 0.3581 (tp) REVERT: C 315 LEU cc_start: 0.9336 (mt) cc_final: 0.9135 (mt) REVERT: D 17 PHE cc_start: 0.5275 (p90) cc_final: 0.4994 (p90) REVERT: D 31 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6961 (pp) REVERT: D 154 PHE cc_start: 0.8253 (t80) cc_final: 0.7944 (t80) REVERT: D 183 LYS cc_start: 0.8470 (mttt) cc_final: 0.8221 (tptt) REVERT: D 242 TYR cc_start: 0.7812 (t80) cc_final: 0.7341 (t80) outliers start: 63 outliers final: 30 residues processed: 548 average time/residue: 0.2969 time to fit residues: 238.9147 Evaluate side-chains 455 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 420 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 232 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.095600 restraints weight = 25540.346| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.79 r_work: 0.2770 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16299 Z= 0.145 Angle : 0.601 13.212 22004 Z= 0.319 Chirality : 0.043 0.181 2348 Planarity : 0.004 0.059 2812 Dihedral : 8.893 163.157 2218 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.74 % Allowed : 18.73 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 1928 helix: 1.38 (0.15), residues: 1145 sheet: 0.11 (0.40), residues: 140 loop : 0.63 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 9 HIS 0.004 0.001 HIS D 254 PHE 0.037 0.002 PHE D 227 TYR 0.029 0.001 TYR C 173 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 896) hydrogen bonds : angle 5.03251 ( 2616) covalent geometry : bond 0.00322 (16298) covalent geometry : angle 0.60102 (22004) Misc. bond : bond 0.00020 ( 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 558 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 511 time to evaluate : 1.662 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 49 HIS cc_start: 0.8647 (m90) cc_final: 0.8316 (m-70) REVERT: A 104 TYR cc_start: 0.9396 (m-80) cc_final: 0.8931 (m-80) REVERT: A 172 LEU cc_start: 0.9519 (mp) cc_final: 0.8921 (mp) REVERT: A 228 LYS cc_start: 0.9321 (mtpp) cc_final: 0.8960 (mtpp) REVERT: A 231 ASP cc_start: 0.9166 (t0) cc_final: 0.8868 (t0) REVERT: A 334 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8589 (ptpt) REVERT: A 336 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9228 (mmtt) REVERT: A 394 TYR cc_start: 0.9425 (m-80) cc_final: 0.9160 (m-80) REVERT: A 406 ASP cc_start: 0.8329 (m-30) cc_final: 0.7916 (t0) REVERT: A 548 GLU cc_start: 0.8821 (tp30) cc_final: 0.8611 (tp30) REVERT: A 659 LYS cc_start: 0.8885 (pttp) cc_final: 0.8649 (pttp) REVERT: B 31 GLU cc_start: 0.8855 (mp0) cc_final: 0.8574 (pm20) REVERT: B 52 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8829 (tptt) REVERT: B 56 ASP cc_start: 0.9037 (m-30) cc_final: 0.8598 (m-30) REVERT: B 75 GLU cc_start: 0.8444 (mp0) cc_final: 0.8107 (mp0) REVERT: B 79 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 150 GLN cc_start: 0.9316 (tp-100) cc_final: 0.9053 (tp-100) REVERT: B 155 THR cc_start: 0.9558 (m) cc_final: 0.9349 (t) REVERT: B 181 ASP cc_start: 0.8910 (m-30) cc_final: 0.8370 (m-30) REVERT: B 276 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8874 (mtpp) REVERT: B 359 MET cc_start: 0.9413 (ttp) cc_final: 0.9089 (tmm) REVERT: B 493 MET cc_start: 0.9551 (tmm) cc_final: 0.9339 (tmm) REVERT: B 586 TYR cc_start: 0.9332 (m-80) cc_final: 0.9123 (m-80) REVERT: B 628 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 681 THR cc_start: 0.9290 (p) cc_final: 0.9068 (p) REVERT: B 686 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8102 (ttm-80) REVERT: C 47 LEU cc_start: 0.5464 (mt) cc_final: 0.4869 (tp) REVERT: C 68 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8334 (mt-10) REVERT: C 93 MET cc_start: 0.8233 (mtt) cc_final: 0.7899 (mtt) REVERT: C 95 MET cc_start: 0.7684 (tmm) cc_final: 0.7381 (tmm) REVERT: C 154 PHE cc_start: 0.9187 (t80) cc_final: 0.8958 (t80) REVERT: C 169 TYR cc_start: 0.8630 (m-80) cc_final: 0.8403 (m-80) REVERT: C 173 TYR cc_start: 0.6000 (t80) cc_final: 0.5604 (t80) REVERT: C 181 GLN cc_start: 0.7723 (mp10) cc_final: 0.7394 (mp10) REVERT: C 184 LEU cc_start: 0.4515 (mt) cc_final: 0.3520 (tt) REVERT: C 193 LEU cc_start: 0.7895 (mt) cc_final: 0.7596 (tt) REVERT: C 212 ILE cc_start: 0.6899 (mm) cc_final: 0.6362 (mm) REVERT: C 252 LEU cc_start: 0.8099 (mp) cc_final: 0.7610 (tt) REVERT: C 273 PHE cc_start: 0.6624 (m-80) cc_final: 0.3654 (t80) REVERT: D 17 PHE cc_start: 0.4864 (p90) cc_final: 0.4573 (p90) REVERT: D 51 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6140 (mm-30) REVERT: D 174 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6442 (t80) REVERT: D 183 LYS cc_start: 0.8426 (mttt) cc_final: 0.8161 (tptt) REVERT: D 227 PHE cc_start: 0.8346 (m-80) cc_final: 0.8081 (m-80) REVERT: D 242 TYR cc_start: 0.7654 (t80) cc_final: 0.7239 (t80) outliers start: 47 outliers final: 24 residues processed: 535 average time/residue: 0.2731 time to fit residues: 214.6229 Evaluate side-chains 478 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 449 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 588 GLN A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 181 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096978 restraints weight = 25530.049| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.82 r_work: 0.2786 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16299 Z= 0.145 Angle : 0.595 13.218 22004 Z= 0.310 Chirality : 0.042 0.159 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.619 158.608 2218 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.03 % Allowed : 19.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1928 helix: 1.34 (0.15), residues: 1146 sheet: -0.05 (0.40), residues: 152 loop : 0.61 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 124 HIS 0.005 0.001 HIS D 254 PHE 0.030 0.002 PHE D 227 TYR 0.019 0.001 TYR C 130 ARG 0.011 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 896) hydrogen bonds : angle 5.00239 ( 2616) covalent geometry : bond 0.00322 (16298) covalent geometry : angle 0.59469 (22004) Misc. bond : bond 0.00111 ( 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 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 469 time to evaluate : 1.878 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 49 HIS cc_start: 0.8612 (m90) cc_final: 0.8330 (m-70) REVERT: A 104 TYR cc_start: 0.9373 (m-80) cc_final: 0.8916 (m-80) REVERT: A 178 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 228 LYS cc_start: 0.9315 (mtpp) cc_final: 0.8956 (mtpp) REVERT: A 266 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8735 (mtmm) REVERT: A 334 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8575 (ptpt) REVERT: A 336 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.9246 (mmtt) REVERT: A 362 ASP cc_start: 0.8665 (m-30) cc_final: 0.8446 (m-30) REVERT: A 384 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: A 394 TYR cc_start: 0.9467 (m-80) cc_final: 0.9093 (m-80) REVERT: A 444 ASP cc_start: 0.8406 (t70) cc_final: 0.7727 (t70) REVERT: A 446 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8392 (mmm160) REVERT: A 548 GLU cc_start: 0.8835 (tp30) cc_final: 0.8622 (tp30) REVERT: B 52 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8847 (tptt) REVERT: B 56 ASP cc_start: 0.9050 (m-30) cc_final: 0.8624 (m-30) REVERT: B 79 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 148 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 150 GLN cc_start: 0.9289 (tp-100) cc_final: 0.9067 (tp-100) REVERT: B 274 ARG cc_start: 0.8021 (ptp90) cc_final: 0.6792 (ptp-170) REVERT: B 276 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8694 (mmtt) REVERT: B 359 MET cc_start: 0.9382 (ttp) cc_final: 0.9117 (tmm) REVERT: B 493 MET cc_start: 0.9558 (tmm) cc_final: 0.9324 (tmm) REVERT: B 586 TYR cc_start: 0.9324 (m-80) cc_final: 0.9122 (m-80) REVERT: B 628 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 681 THR cc_start: 0.9281 (p) cc_final: 0.9057 (p) REVERT: B 686 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.8188 (ttm-80) REVERT: C 68 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8304 (mt-10) REVERT: C 93 MET cc_start: 0.8246 (mtt) cc_final: 0.7866 (mtt) REVERT: C 95 MET cc_start: 0.7794 (tmm) cc_final: 0.7237 (tmm) REVERT: C 96 MET cc_start: 0.8774 (mmm) cc_final: 0.8068 (mmm) REVERT: C 154 PHE cc_start: 0.9188 (t80) cc_final: 0.8963 (t80) REVERT: C 174 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 181 GLN cc_start: 0.7802 (mp-120) cc_final: 0.7515 (mp10) REVERT: C 193 LEU cc_start: 0.7878 (mt) cc_final: 0.7555 (tt) REVERT: C 212 ILE cc_start: 0.7185 (mm) cc_final: 0.6827 (mm) REVERT: C 273 PHE cc_start: 0.6244 (m-80) cc_final: 0.2762 (t80) REVERT: D 29 PHE cc_start: 0.4283 (t80) cc_final: 0.4070 (t80) REVERT: D 227 PHE cc_start: 0.8466 (m-80) cc_final: 0.8145 (m-80) REVERT: D 242 TYR cc_start: 0.7706 (t80) cc_final: 0.7233 (t80) REVERT: D 269 MET cc_start: 0.7007 (ppp) cc_final: 0.6796 (ppp) outliers start: 52 outliers final: 24 residues processed: 492 average time/residue: 0.2783 time to fit residues: 204.4239 Evaluate side-chains 482 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 451 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.090283 restraints weight = 26394.702| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.91 r_work: 0.2665 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 16299 Z= 0.342 Angle : 0.659 12.326 22004 Z= 0.350 Chirality : 0.046 0.145 2348 Planarity : 0.004 0.052 2812 Dihedral : 9.000 164.563 2218 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.44 % Allowed : 20.19 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1928 helix: 1.26 (0.15), residues: 1142 sheet: -0.58 (0.40), residues: 144 loop : 0.51 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 30 HIS 0.006 0.001 HIS A 438 PHE 0.032 0.002 PHE C 259 TYR 0.034 0.002 TYR D 174 ARG 0.007 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 896) hydrogen bonds : angle 5.17895 ( 2616) covalent geometry : bond 0.00768 (16298) covalent geometry : angle 0.65900 (22004) Misc. bond : bond 0.00205 ( 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 509 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 450 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8708 (m90) cc_final: 0.8457 (m-70) REVERT: A 144 MET cc_start: 0.9287 (mtm) cc_final: 0.9027 (mtp) REVERT: A 178 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8882 (p) REVERT: A 286 ASP cc_start: 0.8799 (m-30) cc_final: 0.8420 (m-30) REVERT: A 334 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8784 (ptpt) REVERT: B 52 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.8745 (tptm) REVERT: B 56 ASP cc_start: 0.9064 (m-30) cc_final: 0.8546 (m-30) REVERT: B 75 GLU cc_start: 0.8541 (mp0) cc_final: 0.8232 (mp0) REVERT: B 79 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8299 (mm-30) REVERT: B 148 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 274 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7079 (ptp-170) REVERT: B 276 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8891 (mmtm) REVERT: B 493 MET cc_start: 0.9565 (tmm) cc_final: 0.9356 (tmm) REVERT: B 586 TYR cc_start: 0.9397 (m-80) cc_final: 0.9058 (m-80) REVERT: B 588 GLN cc_start: 0.9453 (mm110) cc_final: 0.8833 (mm-40) REVERT: B 628 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8477 (mt-10) REVERT: B 686 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8320 (ttm-80) REVERT: C 28 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8509 (mm-40) REVERT: C 67 THR cc_start: 0.7501 (t) cc_final: 0.7211 (p) REVERT: C 68 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8268 (mt-10) REVERT: C 74 MET cc_start: 0.8822 (mmm) cc_final: 0.8535 (mmm) REVERT: C 93 MET cc_start: 0.8282 (mtt) cc_final: 0.7856 (mtt) REVERT: C 95 MET cc_start: 0.8027 (tmm) cc_final: 0.7675 (tmm) REVERT: C 154 PHE cc_start: 0.9252 (t80) cc_final: 0.9049 (t80) REVERT: C 174 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7240 (t80) REVERT: C 181 GLN cc_start: 0.7657 (mp-120) cc_final: 0.7363 (mp10) REVERT: C 193 LEU cc_start: 0.7811 (mt) cc_final: 0.7582 (tt) REVERT: C 236 TYR cc_start: 0.7903 (t80) cc_final: 0.7308 (t80) REVERT: C 270 ASN cc_start: 0.8130 (m-40) cc_final: 0.7920 (t0) REVERT: C 273 PHE cc_start: 0.6260 (m-80) cc_final: 0.2742 (t80) REVERT: D 68 GLU cc_start: 0.7178 (tt0) cc_final: 0.6802 (mm-30) REVERT: D 196 ARG cc_start: 0.6484 (tmm-80) cc_final: 0.6120 (ptm-80) REVERT: D 227 PHE cc_start: 0.8398 (m-80) cc_final: 0.8038 (m-80) REVERT: D 242 TYR cc_start: 0.7841 (t80) cc_final: 0.7534 (t80) outliers start: 59 outliers final: 33 residues processed: 479 average time/residue: 0.2803 time to fit residues: 198.8677 Evaluate side-chains 444 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 405 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 232 ASN B 320 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 91 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 = 0.3819 r_free = 0.3819 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096982 restraints weight = 25529.754| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.89 r_work: 0.2780 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16299 Z= 0.146 Angle : 0.604 12.630 22004 Z= 0.314 Chirality : 0.043 0.223 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.602 159.554 2216 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.86 % Allowed : 21.53 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1928 helix: 1.30 (0.15), residues: 1140 sheet: -0.29 (0.41), residues: 152 loop : 0.49 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 44 HIS 0.005 0.001 HIS D 254 PHE 0.032 0.002 PHE C 259 TYR 0.018 0.001 TYR C 130 ARG 0.010 0.001 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 896) hydrogen bonds : angle 4.99686 ( 2616) covalent geometry : bond 0.00326 (16298) covalent geometry : angle 0.60402 (22004) Misc. bond : bond 0.00599 ( 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 503 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 454 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8756 (tppt) cc_final: 0.8508 (tppt) REVERT: A 49 HIS cc_start: 0.8714 (m90) cc_final: 0.8485 (m-70) REVERT: A 104 TYR cc_start: 0.9422 (m-80) cc_final: 0.8818 (m-80) REVERT: A 178 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8964 (p) REVERT: A 228 LYS cc_start: 0.9296 (mtpp) cc_final: 0.8932 (mtpp) REVERT: A 266 LYS cc_start: 0.9007 (mtmm) cc_final: 0.8743 (mtmm) REVERT: A 274 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8145 (ttm-80) REVERT: A 286 ASP cc_start: 0.8812 (m-30) cc_final: 0.8568 (m-30) REVERT: A 334 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8677 (ptpt) REVERT: A 350 ARG cc_start: 0.9463 (mtp85) cc_final: 0.8608 (mtp85) REVERT: A 384 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: A 411 LEU cc_start: 0.9044 (mt) cc_final: 0.8843 (mt) REVERT: A 550 MET cc_start: 0.9029 (mtm) cc_final: 0.8816 (mtt) REVERT: A 595 MET cc_start: 0.8972 (mmm) cc_final: 0.8671 (mmt) REVERT: A 684 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7481 (t80) REVERT: B 52 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.8853 (tptt) REVERT: B 56 ASP cc_start: 0.9012 (m-30) cc_final: 0.8572 (m-30) REVERT: B 75 GLU cc_start: 0.8473 (mp0) cc_final: 0.8101 (mp0) REVERT: B 79 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 274 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6967 (ptp-170) REVERT: B 276 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8816 (mmtt) REVERT: B 493 MET cc_start: 0.9588 (tmm) cc_final: 0.9342 (tmm) REVERT: B 570 MET cc_start: 0.9139 (mtp) cc_final: 0.8790 (tpp) REVERT: B 586 TYR cc_start: 0.9307 (m-80) cc_final: 0.9046 (m-80) REVERT: B 628 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8387 (mt-10) REVERT: B 686 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8322 (ttm-80) REVERT: C 67 THR cc_start: 0.7403 (t) cc_final: 0.7044 (p) REVERT: C 68 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8146 (pt0) REVERT: C 74 MET cc_start: 0.8871 (mmm) cc_final: 0.8646 (mmm) REVERT: C 93 MET cc_start: 0.8197 (mtt) cc_final: 0.7818 (mtt) REVERT: C 95 MET cc_start: 0.7802 (tmm) cc_final: 0.7516 (tmm) REVERT: C 154 PHE cc_start: 0.9200 (t80) cc_final: 0.8969 (t80) REVERT: C 174 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7034 (t80) REVERT: C 181 GLN cc_start: 0.7659 (mp-120) cc_final: 0.7412 (mp10) REVERT: C 212 ILE cc_start: 0.7147 (mm) cc_final: 0.6830 (mm) REVERT: C 240 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7743 (mp) REVERT: C 273 PHE cc_start: 0.6278 (m-80) cc_final: 0.2654 (t80) REVERT: D 68 GLU cc_start: 0.6968 (tt0) cc_final: 0.6533 (mm-30) REVERT: D 227 PHE cc_start: 0.8540 (m-80) cc_final: 0.8269 (m-80) REVERT: D 242 TYR cc_start: 0.7832 (t80) cc_final: 0.7604 (t80) outliers start: 49 outliers final: 25 residues processed: 474 average time/residue: 0.2751 time to fit residues: 193.5582 Evaluate side-chains 460 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 426 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN B 320 ASN C 132 GLN C 263 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 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 = 0.3837 r_free = 0.3837 target = 0.156677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098985 restraints weight = 25692.582| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.86 r_work: 0.2814 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16299 Z= 0.134 Angle : 0.607 12.543 22004 Z= 0.317 Chirality : 0.043 0.195 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.370 155.311 2216 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.28 % Allowed : 22.40 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1928 helix: 1.34 (0.15), residues: 1140 sheet: -0.19 (0.41), residues: 154 loop : 0.42 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 44 HIS 0.004 0.001 HIS D 254 PHE 0.028 0.002 PHE C 259 TYR 0.024 0.001 TYR D 174 ARG 0.010 0.001 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 896) hydrogen bonds : angle 4.93100 ( 2616) covalent geometry : bond 0.00298 (16298) covalent geometry : angle 0.60719 (22004) Misc. bond : bond 0.00252 ( 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 515 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 476 time to evaluate : 1.960 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 104 TYR cc_start: 0.9366 (m-80) cc_final: 0.8922 (m-80) REVERT: A 128 PHE cc_start: 0.9267 (t80) cc_final: 0.9065 (t80) REVERT: A 178 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8997 (p) REVERT: A 228 LYS cc_start: 0.9243 (mtpp) cc_final: 0.8878 (mtpp) REVERT: A 266 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8830 (mtmm) REVERT: A 286 ASP cc_start: 0.8796 (m-30) cc_final: 0.8529 (m-30) REVERT: A 334 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8665 (ptpt) REVERT: A 384 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: A 446 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8521 (mmm160) REVERT: A 595 MET cc_start: 0.8974 (mmm) cc_final: 0.8726 (mmt) REVERT: A 684 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7392 (t80) REVERT: B 52 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8871 (tptt) REVERT: B 56 ASP cc_start: 0.8971 (m-30) cc_final: 0.8525 (m-30) REVERT: B 75 GLU cc_start: 0.8477 (mp0) cc_final: 0.8204 (mp0) REVERT: B 79 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 144 MET cc_start: 0.9214 (mtm) cc_final: 0.8993 (mtp) REVERT: B 150 GLN cc_start: 0.9285 (tp-100) cc_final: 0.9046 (tp40) REVERT: B 184 ARG cc_start: 0.9235 (tpp-160) cc_final: 0.8912 (tpp80) REVERT: B 274 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6951 (ptp-170) REVERT: B 276 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8829 (mmtt) REVERT: B 493 MET cc_start: 0.9558 (tmm) cc_final: 0.9322 (tmm) REVERT: B 570 MET cc_start: 0.9102 (mtp) cc_final: 0.8792 (tpp) REVERT: B 586 TYR cc_start: 0.9259 (m-80) cc_final: 0.9030 (m-80) REVERT: B 589 SER cc_start: 0.9694 (t) cc_final: 0.9332 (p) REVERT: B 686 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8304 (ttm-80) REVERT: C 67 THR cc_start: 0.7734 (t) cc_final: 0.7414 (p) REVERT: C 68 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8183 (pt0) REVERT: C 74 MET cc_start: 0.8860 (mmm) cc_final: 0.8652 (mmm) REVERT: C 93 MET cc_start: 0.8317 (mtt) cc_final: 0.7864 (mtt) REVERT: C 95 MET cc_start: 0.7758 (tmm) cc_final: 0.7488 (tmm) REVERT: C 137 MET cc_start: 0.5772 (mtt) cc_final: 0.5397 (mpp) REVERT: C 149 ASP cc_start: 0.8238 (t70) cc_final: 0.8037 (p0) REVERT: C 174 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7121 (t80) REVERT: C 212 ILE cc_start: 0.7343 (mm) cc_final: 0.7108 (mm) REVERT: C 240 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7586 (mp) REVERT: C 269 MET cc_start: 0.8695 (ptt) cc_final: 0.8462 (ptt) REVERT: C 271 LEU cc_start: 0.8107 (mt) cc_final: 0.7383 (mt) REVERT: C 273 PHE cc_start: 0.6115 (m-80) cc_final: 0.2615 (t80) REVERT: D 68 GLU cc_start: 0.7050 (tt0) cc_final: 0.6556 (mm-30) REVERT: D 218 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8226 (pm20) REVERT: D 227 PHE cc_start: 0.8426 (m-80) cc_final: 0.8186 (m-80) outliers start: 39 outliers final: 27 residues processed: 492 average time/residue: 0.2755 time to fit residues: 202.9482 Evaluate side-chains 463 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 427 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 568 HIS ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099261 restraints weight = 25468.353| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.85 r_work: 0.2807 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16299 Z= 0.152 Angle : 0.614 12.221 22004 Z= 0.321 Chirality : 0.043 0.169 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.255 154.102 2216 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.68 % Allowed : 22.29 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1928 helix: 1.34 (0.15), residues: 1139 sheet: -0.23 (0.41), residues: 154 loop : 0.29 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 44 HIS 0.004 0.001 HIS D 254 PHE 0.025 0.002 PHE C 259 TYR 0.020 0.001 TYR C 46 ARG 0.007 0.001 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 896) hydrogen bonds : angle 4.93082 ( 2616) covalent geometry : bond 0.00347 (16298) covalent geometry : angle 0.61354 (22004) Misc. bond : bond 0.00185 ( 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 488 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 442 time to evaluate : 1.782 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 49 HIS cc_start: 0.8654 (m-70) cc_final: 0.8372 (m90) REVERT: A 104 TYR cc_start: 0.9387 (m-80) cc_final: 0.8864 (m-80) REVERT: A 178 SER cc_start: 0.9279 (OUTLIER) cc_final: 0.8977 (p) REVERT: A 228 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8902 (mtpp) REVERT: A 274 ARG cc_start: 0.8646 (ttm170) cc_final: 0.8316 (ttm170) REVERT: A 286 ASP cc_start: 0.8774 (m-30) cc_final: 0.8400 (m-30) REVERT: A 334 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8623 (ptpt) REVERT: A 384 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: A 684 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7477 (t80) REVERT: B 75 GLU cc_start: 0.8483 (mp0) cc_final: 0.8209 (mp0) REVERT: B 79 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 144 MET cc_start: 0.9294 (mtm) cc_final: 0.9052 (mtp) REVERT: B 150 GLN cc_start: 0.9281 (tp-100) cc_final: 0.9035 (tp-100) REVERT: B 184 ARG cc_start: 0.9247 (tpp-160) cc_final: 0.8956 (tpp80) REVERT: B 263 ASP cc_start: 0.9004 (m-30) cc_final: 0.8571 (m-30) REVERT: B 274 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6958 (ptp-170) REVERT: B 276 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8791 (mmtt) REVERT: B 359 MET cc_start: 0.9459 (ttp) cc_final: 0.9240 (tmm) REVERT: B 493 MET cc_start: 0.9554 (tmm) cc_final: 0.9300 (tmm) REVERT: B 570 MET cc_start: 0.9113 (mtp) cc_final: 0.8780 (tpp) REVERT: B 586 TYR cc_start: 0.9264 (m-80) cc_final: 0.9047 (m-80) REVERT: B 589 SER cc_start: 0.9676 (t) cc_final: 0.9325 (p) REVERT: B 686 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8259 (ttm-80) REVERT: C 17 PHE cc_start: 0.8435 (p90) cc_final: 0.8107 (p90) REVERT: C 67 THR cc_start: 0.7755 (t) cc_final: 0.7456 (p) REVERT: C 68 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8198 (pt0) REVERT: C 93 MET cc_start: 0.8356 (mtt) cc_final: 0.7845 (mtt) REVERT: C 95 MET cc_start: 0.7885 (tmm) cc_final: 0.7583 (tmm) REVERT: C 149 ASP cc_start: 0.8330 (t70) cc_final: 0.8106 (p0) REVERT: C 174 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.7066 (t80) REVERT: C 204 TYR cc_start: 0.8800 (t80) cc_final: 0.8496 (t80) REVERT: C 271 LEU cc_start: 0.8042 (mt) cc_final: 0.7446 (mt) REVERT: C 273 PHE cc_start: 0.6021 (m-80) cc_final: 0.2598 (t80) REVERT: D 68 GLU cc_start: 0.7106 (tt0) cc_final: 0.6585 (mm-30) REVERT: D 124 TRP cc_start: 0.8285 (t-100) cc_final: 0.8080 (t-100) REVERT: D 174 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6519 (t80) REVERT: D 218 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8320 (pm20) REVERT: D 252 LEU cc_start: 0.4404 (mt) cc_final: 0.3703 (mp) outliers start: 46 outliers final: 26 residues processed: 465 average time/residue: 0.2850 time to fit residues: 195.5158 Evaluate side-chains 450 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 416 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.096363 restraints weight = 25595.306| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.83 r_work: 0.2760 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16299 Z= 0.227 Angle : 0.665 13.317 22004 Z= 0.348 Chirality : 0.045 0.245 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.461 156.884 2216 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.51 % Allowed : 22.93 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 1928 helix: 1.18 (0.15), residues: 1144 sheet: 0.02 (0.44), residues: 136 loop : 0.22 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 44 HIS 0.005 0.001 HIS A 438 PHE 0.021 0.002 PHE C 259 TYR 0.020 0.002 TYR C 179 ARG 0.005 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 896) hydrogen bonds : angle 5.04954 ( 2616) covalent geometry : bond 0.00517 (16298) covalent geometry : angle 0.66549 (22004) Misc. bond : bond 0.00158 ( 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 452 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 409 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8719 (tppt) cc_final: 0.8476 (tppt) REVERT: A 49 HIS cc_start: 0.8649 (m-70) cc_final: 0.8427 (m90) REVERT: A 112 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9071 (ptpp) REVERT: A 178 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 228 LYS cc_start: 0.9298 (mtpp) cc_final: 0.8933 (mtpp) REVERT: A 274 ARG cc_start: 0.8629 (ttm170) cc_final: 0.8289 (ttm170) REVERT: A 286 ASP cc_start: 0.8785 (m-30) cc_final: 0.8402 (m-30) REVERT: A 334 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8743 (ptpt) REVERT: A 384 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: A 406 ASP cc_start: 0.8484 (m-30) cc_final: 0.8064 (t0) REVERT: A 684 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7532 (t80) REVERT: B 56 ASP cc_start: 0.9015 (m-30) cc_final: 0.8621 (m-30) REVERT: B 75 GLU cc_start: 0.8466 (mp0) cc_final: 0.8105 (mp0) REVERT: B 79 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 274 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6923 (ptp-170) REVERT: B 276 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8855 (mmtt) REVERT: B 296 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8667 (mmmt) REVERT: B 359 MET cc_start: 0.9463 (ttp) cc_final: 0.9153 (tmm) REVERT: B 493 MET cc_start: 0.9567 (tmm) cc_final: 0.9237 (tmm) REVERT: B 586 TYR cc_start: 0.9303 (m-80) cc_final: 0.9053 (m-80) REVERT: B 589 SER cc_start: 0.9674 (t) cc_final: 0.9332 (p) REVERT: B 686 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8268 (ttm-80) REVERT: C 17 PHE cc_start: 0.8524 (p90) cc_final: 0.8134 (p90) REVERT: C 67 THR cc_start: 0.7696 (t) cc_final: 0.7382 (p) REVERT: C 68 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8279 (pt0) REVERT: C 93 MET cc_start: 0.8251 (mtt) cc_final: 0.7810 (mtt) REVERT: C 95 MET cc_start: 0.7803 (tmm) cc_final: 0.7555 (tmm) REVERT: C 154 PHE cc_start: 0.8999 (t80) cc_final: 0.8517 (m-80) REVERT: C 174 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.7088 (t80) REVERT: C 181 GLN cc_start: 0.7447 (mp10) cc_final: 0.7146 (pm20) REVERT: C 204 TYR cc_start: 0.8836 (t80) cc_final: 0.8531 (t80) REVERT: C 269 MET cc_start: 0.8793 (ptt) cc_final: 0.8449 (ptp) REVERT: C 270 ASN cc_start: 0.8295 (m-40) cc_final: 0.8009 (t0) REVERT: C 271 LEU cc_start: 0.8127 (mt) cc_final: 0.7429 (mt) REVERT: C 273 PHE cc_start: 0.5951 (m-80) cc_final: 0.2524 (t80) REVERT: D 68 GLU cc_start: 0.6845 (tt0) cc_final: 0.6546 (mm-30) REVERT: D 174 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6230 (t80) REVERT: D 218 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8303 (pm20) REVERT: D 252 LEU cc_start: 0.4281 (mt) cc_final: 0.3512 (mp) outliers start: 43 outliers final: 31 residues processed: 430 average time/residue: 0.2827 time to fit residues: 180.2233 Evaluate side-chains 431 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 391 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 129 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099636 restraints weight = 25617.949| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.89 r_work: 0.2817 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16299 Z= 0.139 Angle : 0.658 13.030 22004 Z= 0.339 Chirality : 0.044 0.289 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.563 153.185 2216 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.16 % Allowed : 23.69 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1928 helix: 1.19 (0.15), residues: 1143 sheet: -0.09 (0.43), residues: 144 loop : 0.18 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 44 HIS 0.004 0.001 HIS D 254 PHE 0.058 0.002 PHE D 227 TYR 0.020 0.001 TYR C 179 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 896) hydrogen bonds : angle 4.99918 ( 2616) covalent geometry : bond 0.00317 (16298) covalent geometry : angle 0.65820 (22004) Misc. bond : bond 0.00344 ( 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 468 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 431 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8596 (m-70) cc_final: 0.8304 (m90) REVERT: A 104 TYR cc_start: 0.9357 (m-80) cc_final: 0.8821 (m-80) REVERT: A 178 SER cc_start: 0.9293 (OUTLIER) cc_final: 0.9007 (p) REVERT: A 184 ARG cc_start: 0.9216 (tpp-160) cc_final: 0.8948 (tpp-160) REVERT: A 266 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8614 (mtmm) REVERT: A 274 ARG cc_start: 0.8676 (ttm170) cc_final: 0.8377 (ttm170) REVERT: A 286 ASP cc_start: 0.8726 (m-30) cc_final: 0.8322 (m-30) REVERT: A 334 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8611 (ptpt) REVERT: A 384 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: A 406 ASP cc_start: 0.8414 (m-30) cc_final: 0.7971 (t0) REVERT: A 598 MET cc_start: 0.8912 (tpp) cc_final: 0.8694 (mmm) REVERT: B 75 GLU cc_start: 0.8536 (mp0) cc_final: 0.8243 (mp0) REVERT: B 79 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 99 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8623 (mmmm) REVERT: B 184 ARG cc_start: 0.9199 (tpp-160) cc_final: 0.8992 (tpp80) REVERT: B 274 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7019 (ptp-170) REVERT: B 276 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8780 (mmtt) REVERT: B 296 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8620 (mmmt) REVERT: B 359 MET cc_start: 0.9415 (ttp) cc_final: 0.9168 (tmm) REVERT: B 493 MET cc_start: 0.9511 (tmm) cc_final: 0.9303 (tmm) REVERT: B 570 MET cc_start: 0.9095 (mtp) cc_final: 0.8733 (tpp) REVERT: B 589 SER cc_start: 0.9659 (t) cc_final: 0.9327 (p) REVERT: B 686 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8253 (ttm-80) REVERT: C 17 PHE cc_start: 0.8555 (p90) cc_final: 0.8205 (p90) REVERT: C 67 THR cc_start: 0.7810 (t) cc_final: 0.7514 (p) REVERT: C 68 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8192 (pt0) REVERT: C 93 MET cc_start: 0.8375 (mtt) cc_final: 0.7887 (mtt) REVERT: C 95 MET cc_start: 0.7806 (tmm) cc_final: 0.7500 (tmm) REVERT: C 154 PHE cc_start: 0.8909 (t80) cc_final: 0.8504 (m-80) REVERT: C 174 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.7112 (t80) REVERT: C 204 TYR cc_start: 0.8783 (t80) cc_final: 0.8470 (t80) REVERT: C 244 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9135 (mt-10) REVERT: D 68 GLU cc_start: 0.6770 (tt0) cc_final: 0.6563 (mm-30) REVERT: D 155 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7797 (pptt) REVERT: D 174 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6174 (t80) REVERT: D 269 MET cc_start: 0.6864 (ppp) cc_final: 0.6455 (ppp) outliers start: 37 outliers final: 26 residues processed: 448 average time/residue: 0.2952 time to fit residues: 196.4538 Evaluate side-chains 445 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 412 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN B 232 ASN B 320 ASN B 361 GLN C 263 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094770 restraints weight = 25789.680| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.83 r_work: 0.2752 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5884 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= 0.221 Angle : 0.688 13.216 22004 Z= 0.354 Chirality : 0.046 0.319 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.555 156.152 2216 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 23.80 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1928 helix: 1.16 (0.15), residues: 1132 sheet: -0.22 (0.42), residues: 152 loop : 0.32 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.047 0.002 PHE D 172 TYR 0.021 0.002 TYR C 179 ARG 0.009 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 896) hydrogen bonds : angle 5.08004 ( 2616) covalent geometry : bond 0.00507 (16298) covalent geometry : angle 0.68837 (22004) Misc. bond : bond 0.00627 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9135.68 seconds wall clock time: 157 minutes 27.04 seconds (9447.04 seconds total)