Starting phenix.real_space_refine on Sat Jun 14 07:24:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzm_45071/06_2025/9bzm_45071_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzm_45071/06_2025/9bzm_45071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzm_45071/06_2025/9bzm_45071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzm_45071/06_2025/9bzm_45071.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzm_45071/06_2025/9bzm_45071_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzm_45071/06_2025/9bzm_45071_neut.cif" } resolution = 4.19 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 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 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: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 9.49, per 1000 atoms: 0.59 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 127.764, 130.806, 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 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 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=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A 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 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A 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 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A 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 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A 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 422 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 475 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 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A 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 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.646A 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 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A 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 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' 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 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 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: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) 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 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 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: 5.72 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4888 1.34 - 1.46: 3062 1.46 - 1.58: 8255 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+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 1.03e+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 9.00e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.570 -0.033 1.17e-02 7.31e+03 7.75e+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 6.95e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21574 2.09 - 4.18: 517 4.18 - 6.27: 37 6.27 - 8.36: 2 8.36 - 10.45: 4 Bond angle restraints: 22134 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 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.13 -4.42 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.30e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.88 -4.38 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9468 35.81 - 71.63: 339 71.63 - 107.44: 37 107.44 - 143.25: 3 143.25 - 179.06: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.75 -179.06 1 2.00e+01 2.50e-03 4.80e+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 301.68 151.18 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.90 148.07 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2139 0.093 - 0.186: 187 0.186 - 0.278: 29 0.278 - 0.371: 3 0.371 - 0.464: 2 Chirality restraints: 2360 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 5.38e+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 4.54e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 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 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11557 3.11 - 3.70: 27051 3.70 - 4.30: 41544 4.30 - 4.90: 65430 Nonbonded interactions: 145713 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 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 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145708 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' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.700 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 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 : 0.006 0.060 16386 Z= 0.315 Angle : 0.740 10.446 22134 Z= 0.463 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 179.065 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % 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: 0.56 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 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 C 227 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51745 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74013 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 976 time to evaluate : 1.785 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: 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 41 ILE cc_start: 0.8814 (mm) cc_final: 0.8409 (mm) REVERT: A 69 LEU cc_start: 0.8277 (mt) cc_final: 0.8076 (mt) REVERT: A 147 GLN cc_start: 0.8267 (mt0) cc_final: 0.7400 (mt0) REVERT: A 171 PHE cc_start: 0.8520 (m-80) cc_final: 0.8253 (m-10) REVERT: A 172 LEU cc_start: 0.9471 (mp) cc_final: 0.9238 (mp) REVERT: A 179 LEU cc_start: 0.8863 (tp) cc_final: 0.8640 (tp) REVERT: A 181 ASP cc_start: 0.8374 (m-30) cc_final: 0.7893 (m-30) REVERT: A 188 ILE cc_start: 0.9195 (mt) cc_final: 0.8964 (mt) REVERT: A 192 LEU cc_start: 0.9448 (mt) cc_final: 0.9072 (mt) REVERT: A 204 SER cc_start: 0.9104 (m) cc_final: 0.8822 (p) REVERT: A 211 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6468 (mm-30) REVERT: A 224 VAL cc_start: 0.8631 (t) cc_final: 0.8368 (p) REVERT: A 258 ILE cc_start: 0.9037 (tp) cc_final: 0.8620 (tp) REVERT: A 278 LEU cc_start: 0.8477 (tp) cc_final: 0.8206 (tp) REVERT: A 294 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6804 (mt-10) REVERT: A 322 MET cc_start: 0.8112 (mmp) cc_final: 0.7424 (mmm) REVERT: A 345 LYS cc_start: 0.8603 (tttt) cc_final: 0.8237 (tttt) REVERT: A 349 LEU cc_start: 0.7857 (mt) cc_final: 0.7549 (mt) REVERT: A 362 ASP cc_start: 0.6167 (m-30) cc_final: 0.5640 (m-30) REVERT: A 407 ILE cc_start: 0.9091 (mt) cc_final: 0.8452 (mt) REVERT: A 417 LEU cc_start: 0.8546 (tt) cc_final: 0.8150 (tt) REVERT: A 420 MET cc_start: 0.8019 (mmm) cc_final: 0.7729 (mmm) REVERT: A 430 LYS cc_start: 0.8978 (mttt) cc_final: 0.8716 (mtpp) REVERT: A 436 LEU cc_start: 0.9196 (mt) cc_final: 0.8942 (mt) REVERT: A 442 THR cc_start: 0.8962 (p) cc_final: 0.8736 (m) REVERT: A 474 GLN cc_start: 0.8573 (mt0) cc_final: 0.8192 (mt0) REVERT: A 494 MET cc_start: 0.8146 (mtp) cc_final: 0.7791 (mtm) REVERT: A 500 ILE cc_start: 0.9349 (mt) cc_final: 0.9136 (mt) REVERT: A 556 GLU cc_start: 0.6880 (tp30) cc_final: 0.6407 (tp30) REVERT: A 558 TRP cc_start: 0.8988 (m100) cc_final: 0.8762 (m100) REVERT: A 571 TYR cc_start: 0.8186 (t80) cc_final: 0.7399 (t80) REVERT: A 573 SER cc_start: 0.9425 (p) cc_final: 0.8956 (p) REVERT: A 587 VAL cc_start: 0.8999 (t) cc_final: 0.8695 (t) REVERT: A 594 VAL cc_start: 0.9180 (m) cc_final: 0.8954 (m) REVERT: A 597 ILE cc_start: 0.9037 (pt) cc_final: 0.8810 (pt) REVERT: A 618 LEU cc_start: 0.9165 (tp) cc_final: 0.8883 (tp) REVERT: A 634 MET cc_start: 0.8111 (mmp) cc_final: 0.7743 (mmm) REVERT: A 644 ILE cc_start: 0.8686 (mt) cc_final: 0.7844 (mt) REVERT: A 653 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 655 THR cc_start: 0.9153 (m) cc_final: 0.8901 (t) REVERT: A 657 PHE cc_start: 0.7945 (m-80) cc_final: 0.7487 (m-80) REVERT: A 667 LEU cc_start: 0.8211 (tt) cc_final: 0.7961 (tt) REVERT: B 11 GLN cc_start: 0.7854 (mt0) cc_final: 0.6869 (mt0) REVERT: B 12 LEU cc_start: 0.9071 (mt) cc_final: 0.8790 (mt) REVERT: B 25 GLN cc_start: 0.7229 (mt0) cc_final: 0.6492 (mt0) REVERT: B 51 LEU cc_start: 0.8138 (tp) cc_final: 0.7822 (tp) REVERT: B 89 PHE cc_start: 0.7544 (t80) cc_final: 0.6840 (t80) REVERT: B 122 ILE cc_start: 0.9370 (mt) cc_final: 0.8930 (mt) REVERT: B 149 TYR cc_start: 0.8400 (t80) cc_final: 0.8048 (t80) REVERT: B 171 PHE cc_start: 0.8787 (m-80) cc_final: 0.8527 (m-80) REVERT: B 181 ASP cc_start: 0.8563 (m-30) cc_final: 0.8330 (m-30) REVERT: B 186 ILE cc_start: 0.9054 (mt) cc_final: 0.8830 (mt) REVERT: B 192 LEU cc_start: 0.9264 (mt) cc_final: 0.8633 (mt) REVERT: B 202 ASN cc_start: 0.8817 (t0) cc_final: 0.8044 (p0) REVERT: B 211 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6023 (mm-30) REVERT: B 232 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7391 (t0) REVERT: B 256 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7515 (tmt-80) REVERT: B 258 ILE cc_start: 0.8587 (tp) cc_final: 0.8377 (tp) REVERT: B 278 LEU cc_start: 0.8728 (tp) cc_final: 0.8246 (tp) REVERT: B 322 MET cc_start: 0.8012 (mmm) cc_final: 0.6237 (tpp) REVERT: B 332 VAL cc_start: 0.8875 (t) cc_final: 0.8630 (t) REVERT: B 345 LYS cc_start: 0.8630 (tttt) cc_final: 0.8110 (tttt) REVERT: B 362 ASP cc_start: 0.6716 (m-30) cc_final: 0.5822 (m-30) REVERT: B 364 VAL cc_start: 0.8922 (t) cc_final: 0.8523 (t) REVERT: B 381 LEU cc_start: 0.9084 (tp) cc_final: 0.8825 (tp) REVERT: B 384 GLU cc_start: 0.8761 (pm20) cc_final: 0.8480 (pm20) REVERT: B 403 ILE cc_start: 0.9387 (mm) cc_final: 0.8913 (mp) REVERT: B 446 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6881 (mtp85) REVERT: B 453 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8086 (ttp80) REVERT: B 505 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6741 (mt-10) REVERT: B 550 MET cc_start: 0.7400 (mtm) cc_final: 0.5932 (mtp) REVERT: B 558 TRP cc_start: 0.8293 (m100) cc_final: 0.7917 (m100) REVERT: B 570 MET cc_start: 0.7401 (mtm) cc_final: 0.6940 (mtm) REVERT: B 587 VAL cc_start: 0.8816 (t) cc_final: 0.8545 (t) REVERT: B 656 LEU cc_start: 0.8446 (mt) cc_final: 0.8210 (mt) REVERT: C 42 LEU cc_start: 0.6344 (mt) cc_final: 0.5906 (mt) REVERT: C 90 LEU cc_start: 0.5256 (mt) cc_final: 0.4765 (mt) REVERT: C 153 LEU cc_start: 0.5389 (tp) cc_final: 0.5091 (tt) REVERT: D 96 MET cc_start: 0.2343 (mmm) cc_final: 0.2061 (mmt) REVERT: D 286 VAL cc_start: 0.7829 (t) cc_final: 0.7036 (p) REVERT: D 317 ASP cc_start: 0.7176 (t0) cc_final: 0.6880 (t0) REVERT: D 321 TYR cc_start: 0.6487 (m-80) cc_final: 0.5317 (m-10) outliers start: 22 outliers final: 7 residues processed: 988 average time/residue: 0.3142 time to fit residues: 439.6613 Evaluate side-chains 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 675 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 43 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 304 HIS A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN A 645 GLN B 11 GLN B 19 GLN B 61 ASN B 218 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 645 GLN B 676 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097481 restraints weight = 36894.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101055 restraints weight = 19614.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103371 restraints weight = 12491.786| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16386 Z= 0.172 Angle : 0.635 7.361 22134 Z= 0.342 Chirality : 0.044 0.299 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.453 179.603 2242 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.17 % Allowed : 2.51 % Favored : 97.32 % 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: 1.19 (0.18), residues: 1932 helix: 1.19 (0.15), residues: 1128 sheet: 0.18 (0.43), residues: 126 loop : 0.43 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 44 HIS 0.007 0.001 HIS A 438 PHE 0.031 0.002 PHE D 320 TYR 0.029 0.002 TYR A 498 ARG 0.008 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 871) hydrogen bonds : angle 5.07134 ( 2571) covalent geometry : bond 0.00370 (16386) covalent geometry : angle 0.63520 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 780 time to evaluate : 1.928 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 28 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8819 (mmmm) REVERT: A 31 GLU cc_start: 0.9422 (tp30) cc_final: 0.9006 (tp30) REVERT: A 41 ILE cc_start: 0.9541 (mm) cc_final: 0.9316 (mm) REVERT: A 54 LYS cc_start: 0.9632 (ttmm) cc_final: 0.9249 (ttmm) REVERT: A 87 LYS cc_start: 0.9511 (tptt) cc_final: 0.9193 (mmmm) REVERT: A 101 TYR cc_start: 0.9258 (m-10) cc_final: 0.8984 (m-10) REVERT: A 120 ASP cc_start: 0.9061 (m-30) cc_final: 0.8748 (m-30) REVERT: A 142 ASN cc_start: 0.9411 (m-40) cc_final: 0.9136 (m110) REVERT: A 147 GLN cc_start: 0.8923 (mt0) cc_final: 0.8583 (mt0) REVERT: A 181 ASP cc_start: 0.9002 (m-30) cc_final: 0.8601 (m-30) REVERT: A 202 ASN cc_start: 0.9597 (t0) cc_final: 0.9257 (t0) REVERT: A 204 SER cc_start: 0.9439 (m) cc_final: 0.8835 (p) REVERT: A 251 LEU cc_start: 0.9595 (tp) cc_final: 0.9314 (tp) REVERT: A 257 ASP cc_start: 0.9058 (m-30) cc_final: 0.8025 (m-30) REVERT: A 286 ASP cc_start: 0.8739 (m-30) cc_final: 0.8189 (m-30) REVERT: A 293 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8575 (ttp80) REVERT: A 337 ILE cc_start: 0.9455 (tp) cc_final: 0.9136 (tp) REVERT: A 344 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8620 (mt-10) REVERT: A 348 MET cc_start: 0.8980 (ptp) cc_final: 0.8674 (ptp) REVERT: A 349 LEU cc_start: 0.9569 (mt) cc_final: 0.9286 (mt) REVERT: A 362 ASP cc_start: 0.8102 (m-30) cc_final: 0.7519 (m-30) REVERT: A 370 ASN cc_start: 0.9333 (m-40) cc_final: 0.8985 (m110) REVERT: A 387 GLN cc_start: 0.8984 (mt0) cc_final: 0.8773 (mt0) REVERT: A 405 LEU cc_start: 0.9164 (mt) cc_final: 0.8910 (mt) REVERT: A 407 ILE cc_start: 0.9205 (mt) cc_final: 0.8802 (mt) REVERT: A 421 GLU cc_start: 0.8214 (pp20) cc_final: 0.8007 (pp20) REVERT: A 443 THR cc_start: 0.9302 (m) cc_final: 0.9065 (t) REVERT: A 458 MET cc_start: 0.9177 (mmp) cc_final: 0.8727 (mmp) REVERT: A 505 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8932 (mt-10) REVERT: A 550 MET cc_start: 0.7679 (mtt) cc_final: 0.6790 (mtt) REVERT: A 573 SER cc_start: 0.9484 (p) cc_final: 0.9163 (p) REVERT: A 584 ILE cc_start: 0.9601 (pt) cc_final: 0.9087 (pt) REVERT: A 588 GLN cc_start: 0.9352 (mm-40) cc_final: 0.9063 (tp40) REVERT: A 599 GLU cc_start: 0.8350 (mp0) cc_final: 0.7832 (mp0) REVERT: A 615 MET cc_start: 0.9009 (mmp) cc_final: 0.8767 (mmp) REVERT: A 630 TYR cc_start: 0.7849 (m-80) cc_final: 0.7034 (m-10) REVERT: A 632 MET cc_start: 0.8896 (mtm) cc_final: 0.8606 (mtp) REVERT: A 645 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8183 (tp-100) REVERT: A 648 ILE cc_start: 0.9541 (mm) cc_final: 0.9166 (mm) REVERT: A 650 GLN cc_start: 0.8590 (mt0) cc_final: 0.8107 (mt0) REVERT: A 654 PHE cc_start: 0.9469 (t80) cc_final: 0.9212 (t80) REVERT: A 655 THR cc_start: 0.9306 (m) cc_final: 0.8744 (t) REVERT: A 664 THR cc_start: 0.9168 (p) cc_final: 0.8642 (p) REVERT: A 667 LEU cc_start: 0.9380 (tt) cc_final: 0.9069 (tt) REVERT: A 668 ASN cc_start: 0.9263 (m110) cc_final: 0.8935 (m110) REVERT: A 677 ARG cc_start: 0.9366 (mmm-85) cc_final: 0.9106 (mmm-85) REVERT: A 680 LYS cc_start: 0.8908 (mttt) cc_final: 0.8426 (mttp) REVERT: A 686 ARG cc_start: 0.8446 (mmt180) cc_final: 0.8087 (mtt-85) REVERT: B 51 LEU cc_start: 0.9500 (tp) cc_final: 0.9226 (tp) REVERT: B 58 LEU cc_start: 0.9671 (mt) cc_final: 0.9452 (mt) REVERT: B 65 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8301 (mp0) REVERT: B 87 LYS cc_start: 0.9267 (tptp) cc_final: 0.8728 (tptp) REVERT: B 123 SER cc_start: 0.9294 (m) cc_final: 0.9019 (m) REVERT: B 147 GLN cc_start: 0.9100 (mt0) cc_final: 0.8674 (mt0) REVERT: B 149 TYR cc_start: 0.9151 (t80) cc_final: 0.8680 (t80) REVERT: B 181 ASP cc_start: 0.9159 (m-30) cc_final: 0.8873 (m-30) REVERT: B 202 ASN cc_start: 0.9560 (t0) cc_final: 0.9324 (t0) REVERT: B 214 LYS cc_start: 0.9261 (mtpp) cc_final: 0.9026 (mmmm) REVERT: B 235 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8701 (ttm-80) REVERT: B 257 ASP cc_start: 0.9004 (m-30) cc_final: 0.8642 (m-30) REVERT: B 278 LEU cc_start: 0.9297 (tp) cc_final: 0.9026 (tp) REVERT: B 279 SER cc_start: 0.8560 (m) cc_final: 0.7849 (p) REVERT: B 316 GLU cc_start: 0.9136 (tt0) cc_final: 0.8906 (tt0) REVERT: B 333 LYS cc_start: 0.9209 (tptp) cc_final: 0.8770 (tttm) REVERT: B 367 VAL cc_start: 0.9720 (m) cc_final: 0.9348 (p) REVERT: B 381 LEU cc_start: 0.9166 (tp) cc_final: 0.8855 (tp) REVERT: B 413 SER cc_start: 0.9545 (m) cc_final: 0.9031 (t) REVERT: B 415 ASN cc_start: 0.9688 (t0) cc_final: 0.9408 (t0) REVERT: B 458 MET cc_start: 0.9504 (mmm) cc_final: 0.9176 (mmp) REVERT: B 459 LYS cc_start: 0.9268 (mttm) cc_final: 0.9053 (mttp) REVERT: B 460 SER cc_start: 0.8947 (t) cc_final: 0.8671 (t) REVERT: B 471 TYR cc_start: 0.9344 (t80) cc_final: 0.8994 (t80) REVERT: B 493 MET cc_start: 0.9469 (tmm) cc_final: 0.9254 (tmm) REVERT: B 505 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 558 TRP cc_start: 0.9314 (m100) cc_final: 0.8447 (m100) REVERT: B 570 MET cc_start: 0.9113 (mtp) cc_final: 0.8627 (mtp) REVERT: B 588 GLN cc_start: 0.9425 (mm-40) cc_final: 0.9176 (mm-40) REVERT: B 599 GLU cc_start: 0.8735 (pt0) cc_final: 0.8458 (pt0) REVERT: B 601 ILE cc_start: 0.9429 (mm) cc_final: 0.9068 (mm) REVERT: B 612 TYR cc_start: 0.8460 (m-10) cc_final: 0.8234 (m-10) REVERT: B 632 MET cc_start: 0.8706 (mtt) cc_final: 0.8053 (mtt) REVERT: B 667 LEU cc_start: 0.9365 (tp) cc_final: 0.9158 (tp) REVERT: C 42 LEU cc_start: 0.9051 (mt) cc_final: 0.8834 (mt) REVERT: C 47 LEU cc_start: 0.7232 (mt) cc_final: 0.7023 (mp) REVERT: C 117 THR cc_start: 0.9009 (p) cc_final: 0.8714 (p) REVERT: C 119 ASN cc_start: 0.9081 (t0) cc_final: 0.8814 (t0) REVERT: C 179 TYR cc_start: 0.8621 (t80) cc_final: 0.8340 (t80) REVERT: D 37 LEU cc_start: 0.5154 (tp) cc_final: 0.2375 (tp) REVERT: D 252 LEU cc_start: 0.8781 (mt) cc_final: 0.8519 (mt) outliers start: 3 outliers final: 1 residues processed: 781 average time/residue: 0.2842 time to fit residues: 325.0007 Evaluate side-chains 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 623 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 19 GLN A 25 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 338 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 361 GLN B 387 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 25 ASN D 181 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096537 restraints weight = 35212.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099369 restraints weight = 20240.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101634 restraints weight = 13546.327| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.211 Angle : 0.632 10.978 22134 Z= 0.335 Chirality : 0.043 0.270 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.060 171.378 2242 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.29 % Allowed : 2.21 % Favored : 97.49 % 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: 1932 helix: 1.26 (0.15), residues: 1132 sheet: -0.09 (0.41), residues: 146 loop : 0.39 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 9 HIS 0.008 0.001 HIS C 254 PHE 0.025 0.002 PHE D 320 TYR 0.023 0.002 TYR C 174 ARG 0.010 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 871) hydrogen bonds : angle 4.94738 ( 2571) covalent geometry : bond 0.00449 (16386) covalent geometry : angle 0.63158 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 692 time to evaluate : 1.900 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 51 LEU cc_start: 0.9592 (tp) cc_final: 0.9323 (pt) REVERT: A 54 LYS cc_start: 0.9722 (ttmm) cc_final: 0.9267 (ttmm) REVERT: A 64 TYR cc_start: 0.8945 (m-10) cc_final: 0.8527 (m-80) REVERT: A 87 LYS cc_start: 0.9518 (tptt) cc_final: 0.9181 (mmmm) REVERT: A 107 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8806 (mtpp) REVERT: A 118 TYR cc_start: 0.9182 (t80) cc_final: 0.8944 (t80) REVERT: A 120 ASP cc_start: 0.9213 (m-30) cc_final: 0.8887 (m-30) REVERT: A 124 ILE cc_start: 0.9766 (mm) cc_final: 0.9551 (mm) REVERT: A 139 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9125 (mt-10) REVERT: A 142 ASN cc_start: 0.9406 (m-40) cc_final: 0.9121 (m110) REVERT: A 150 GLN cc_start: 0.9268 (tm-30) cc_final: 0.9028 (tm-30) REVERT: A 168 VAL cc_start: 0.9265 (t) cc_final: 0.9000 (m) REVERT: A 175 VAL cc_start: 0.9534 (t) cc_final: 0.9333 (t) REVERT: A 181 ASP cc_start: 0.8991 (m-30) cc_final: 0.8614 (m-30) REVERT: A 184 ARG cc_start: 0.9168 (tpp-160) cc_final: 0.8944 (tpp-160) REVERT: A 223 VAL cc_start: 0.9498 (m) cc_final: 0.9181 (p) REVERT: A 227 MET cc_start: 0.9369 (mtp) cc_final: 0.8938 (mtp) REVERT: A 251 LEU cc_start: 0.9707 (tp) cc_final: 0.9404 (tp) REVERT: A 263 ASP cc_start: 0.9198 (m-30) cc_final: 0.8873 (m-30) REVERT: A 286 ASP cc_start: 0.8537 (m-30) cc_final: 0.8099 (m-30) REVERT: A 316 GLU cc_start: 0.8928 (pt0) cc_final: 0.8619 (pp20) REVERT: A 322 MET cc_start: 0.8968 (mmp) cc_final: 0.7956 (mmm) REVERT: A 337 ILE cc_start: 0.9425 (tp) cc_final: 0.9213 (tp) REVERT: A 344 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 348 MET cc_start: 0.8993 (ptp) cc_final: 0.8709 (ptp) REVERT: A 349 LEU cc_start: 0.9608 (mt) cc_final: 0.9316 (mt) REVERT: A 362 ASP cc_start: 0.8155 (m-30) cc_final: 0.7510 (m-30) REVERT: A 370 ASN cc_start: 0.9487 (m-40) cc_final: 0.9202 (m-40) REVERT: A 402 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 403 ILE cc_start: 0.9139 (mm) cc_final: 0.8849 (mm) REVERT: A 405 LEU cc_start: 0.9109 (mt) cc_final: 0.8754 (mp) REVERT: A 407 ILE cc_start: 0.9345 (mt) cc_final: 0.9023 (mt) REVERT: A 421 GLU cc_start: 0.8487 (pp20) cc_final: 0.8259 (pp20) REVERT: A 443 THR cc_start: 0.9435 (m) cc_final: 0.9202 (t) REVERT: A 485 ARG cc_start: 0.9195 (mtm-85) cc_final: 0.8862 (mtm-85) REVERT: A 490 THR cc_start: 0.9674 (m) cc_final: 0.9360 (p) REVERT: A 505 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8865 (mt-10) REVERT: A 516 GLN cc_start: 0.9493 (mt0) cc_final: 0.8811 (tp-100) REVERT: A 552 ILE cc_start: 0.9549 (mp) cc_final: 0.9284 (mp) REVERT: A 601 ILE cc_start: 0.9536 (mm) cc_final: 0.9334 (tp) REVERT: A 630 TYR cc_start: 0.8473 (m-80) cc_final: 0.7132 (m-80) REVERT: A 632 MET cc_start: 0.8884 (mtm) cc_final: 0.8632 (mtp) REVERT: A 639 ASP cc_start: 0.9131 (m-30) cc_final: 0.8813 (m-30) REVERT: A 645 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8674 (tp-100) REVERT: A 650 GLN cc_start: 0.8487 (mt0) cc_final: 0.7923 (mt0) REVERT: A 664 THR cc_start: 0.9375 (p) cc_final: 0.8599 (p) REVERT: A 667 LEU cc_start: 0.9486 (tt) cc_final: 0.9244 (tt) REVERT: A 668 ASN cc_start: 0.9350 (m110) cc_final: 0.9002 (m110) REVERT: A 686 ARG cc_start: 0.8743 (mmt180) cc_final: 0.8346 (mmt-90) REVERT: B 58 LEU cc_start: 0.9675 (mt) cc_final: 0.9449 (mt) REVERT: B 87 LYS cc_start: 0.9353 (tptp) cc_final: 0.9007 (tptp) REVERT: B 106 LEU cc_start: 0.9339 (tt) cc_final: 0.9116 (tt) REVERT: B 116 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8338 (mp0) REVERT: B 117 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8695 (ttm110) REVERT: B 120 ASP cc_start: 0.8847 (m-30) cc_final: 0.8597 (m-30) REVERT: B 147 GLN cc_start: 0.9022 (mt0) cc_final: 0.8698 (mt0) REVERT: B 149 TYR cc_start: 0.9194 (t80) cc_final: 0.8872 (t80) REVERT: B 158 ASN cc_start: 0.9330 (m110) cc_final: 0.9119 (m-40) REVERT: B 172 LEU cc_start: 0.9331 (mp) cc_final: 0.9020 (mp) REVERT: B 191 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8621 (mm-40) REVERT: B 211 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8621 (mm-30) REVERT: B 227 MET cc_start: 0.9077 (mtt) cc_final: 0.8595 (mtt) REVERT: B 232 ASN cc_start: 0.8993 (t160) cc_final: 0.8517 (t0) REVERT: B 257 ASP cc_start: 0.9045 (m-30) cc_final: 0.8735 (m-30) REVERT: B 278 LEU cc_start: 0.9325 (tp) cc_final: 0.9097 (tp) REVERT: B 279 SER cc_start: 0.8395 (m) cc_final: 0.7825 (p) REVERT: B 319 MET cc_start: 0.9264 (tpp) cc_final: 0.8716 (tpp) REVERT: B 322 MET cc_start: 0.9084 (mmm) cc_final: 0.8336 (mmm) REVERT: B 333 LYS cc_start: 0.9349 (tptp) cc_final: 0.8882 (tttm) REVERT: B 378 PHE cc_start: 0.9373 (p90) cc_final: 0.9134 (p90) REVERT: B 381 LEU cc_start: 0.9322 (tp) cc_final: 0.9076 (tp) REVERT: B 398 ASP cc_start: 0.8898 (t0) cc_final: 0.8679 (t0) REVERT: B 407 ILE cc_start: 0.9381 (mt) cc_final: 0.8954 (mt) REVERT: B 413 SER cc_start: 0.9563 (m) cc_final: 0.9060 (t) REVERT: B 415 ASN cc_start: 0.9632 (t0) cc_final: 0.9342 (t0) REVERT: B 458 MET cc_start: 0.9557 (mmm) cc_final: 0.9204 (mmp) REVERT: B 459 LYS cc_start: 0.9245 (mttm) cc_final: 0.8424 (mtmt) REVERT: B 472 LEU cc_start: 0.9726 (mt) cc_final: 0.9486 (mt) REVERT: B 474 GLN cc_start: 0.8665 (mm110) cc_final: 0.8075 (mm-40) REVERT: B 493 MET cc_start: 0.9470 (tmm) cc_final: 0.9159 (tmm) REVERT: B 505 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 599 GLU cc_start: 0.8728 (pt0) cc_final: 0.8446 (pt0) REVERT: B 604 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8929 (ttm-80) REVERT: B 640 MET cc_start: 0.9304 (tpp) cc_final: 0.9087 (tpp) REVERT: B 658 LEU cc_start: 0.9570 (mt) cc_final: 0.9360 (mt) REVERT: C 179 TYR cc_start: 0.8679 (t80) cc_final: 0.8348 (t80) REVERT: D 69 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8508 (tm-30) REVERT: D 137 MET cc_start: 0.5289 (mmm) cc_final: 0.4782 (mpp) REVERT: D 158 VAL cc_start: 0.8849 (t) cc_final: 0.7610 (t) REVERT: D 162 TYR cc_start: 0.8628 (m-10) cc_final: 0.8355 (m-80) REVERT: D 233 ASN cc_start: 0.8789 (m110) cc_final: 0.8087 (m110) REVERT: D 278 GLU cc_start: 0.8255 (pp20) cc_final: 0.7977 (pp20) outliers start: 5 outliers final: 0 residues processed: 694 average time/residue: 0.2715 time to fit residues: 278.4281 Evaluate side-chains 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 0.0070 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 338 ASN A 361 GLN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098655 restraints weight = 38600.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102224 restraints weight = 20312.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104507 restraints weight = 12885.210| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.135 Angle : 0.584 8.662 22134 Z= 0.309 Chirality : 0.042 0.208 2360 Planarity : 0.003 0.039 2818 Dihedral : 10.795 167.811 2242 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1133 sheet: -0.03 (0.41), residues: 148 loop : 0.17 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 9 HIS 0.005 0.001 HIS B 438 PHE 0.039 0.002 PHE D 168 TYR 0.019 0.001 TYR D 130 ARG 0.009 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 871) hydrogen bonds : angle 4.79603 ( 2571) covalent geometry : bond 0.00295 (16386) covalent geometry : angle 0.58406 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 704 time to evaluate : 1.777 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: A 41 ILE cc_start: 0.9551 (mm) cc_final: 0.9201 (mm) REVERT: A 51 LEU cc_start: 0.9544 (tp) cc_final: 0.9324 (pt) REVERT: A 54 LYS cc_start: 0.9734 (ttmm) cc_final: 0.9304 (ttmm) REVERT: A 64 TYR cc_start: 0.8964 (m-10) cc_final: 0.8593 (m-80) REVERT: A 65 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8367 (mm-30) REVERT: A 87 LYS cc_start: 0.9522 (tptt) cc_final: 0.9264 (mmmm) REVERT: A 107 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8599 (mtpp) REVERT: A 118 TYR cc_start: 0.9251 (t80) cc_final: 0.8931 (t80) REVERT: A 120 ASP cc_start: 0.9083 (m-30) cc_final: 0.8811 (m-30) REVERT: A 139 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9055 (mt-10) REVERT: A 142 ASN cc_start: 0.9430 (m-40) cc_final: 0.9141 (m110) REVERT: A 147 GLN cc_start: 0.9129 (mt0) cc_final: 0.8805 (mt0) REVERT: A 150 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 157 LEU cc_start: 0.9449 (tp) cc_final: 0.9159 (tp) REVERT: A 168 VAL cc_start: 0.9167 (t) cc_final: 0.8891 (m) REVERT: A 171 PHE cc_start: 0.9356 (m-10) cc_final: 0.9108 (m-10) REVERT: A 175 VAL cc_start: 0.9518 (t) cc_final: 0.9289 (t) REVERT: A 223 VAL cc_start: 0.9538 (m) cc_final: 0.9192 (p) REVERT: A 227 MET cc_start: 0.9379 (mtp) cc_final: 0.8887 (mtp) REVERT: A 228 LYS cc_start: 0.9479 (mmmm) cc_final: 0.9015 (tppt) REVERT: A 251 LEU cc_start: 0.9677 (tp) cc_final: 0.9376 (tp) REVERT: A 268 SER cc_start: 0.9093 (p) cc_final: 0.8649 (m) REVERT: A 286 ASP cc_start: 0.8708 (m-30) cc_final: 0.8265 (m-30) REVERT: A 290 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 291 LEU cc_start: 0.9373 (mp) cc_final: 0.8896 (mt) REVERT: A 321 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 322 MET cc_start: 0.9064 (mmp) cc_final: 0.8080 (mmm) REVERT: A 333 LYS cc_start: 0.9100 (tptp) cc_final: 0.8766 (tptp) REVERT: A 344 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8677 (mt-10) REVERT: A 348 MET cc_start: 0.8936 (ptp) cc_final: 0.8701 (ptp) REVERT: A 349 LEU cc_start: 0.9546 (mt) cc_final: 0.9273 (mt) REVERT: A 361 GLN cc_start: 0.8864 (tp40) cc_final: 0.7837 (tp-100) REVERT: A 362 ASP cc_start: 0.8131 (m-30) cc_final: 0.7392 (m-30) REVERT: A 365 ASN cc_start: 0.9110 (m110) cc_final: 0.7820 (m-40) REVERT: A 370 ASN cc_start: 0.9514 (m-40) cc_final: 0.9270 (m-40) REVERT: A 375 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8809 (mtmm) REVERT: A 403 ILE cc_start: 0.9217 (mm) cc_final: 0.8924 (mm) REVERT: A 407 ILE cc_start: 0.9365 (mt) cc_final: 0.9039 (mt) REVERT: A 421 GLU cc_start: 0.8310 (pp20) cc_final: 0.8070 (pp20) REVERT: A 458 MET cc_start: 0.9424 (mmp) cc_final: 0.9102 (mmp) REVERT: A 490 THR cc_start: 0.9627 (m) cc_final: 0.9397 (p) REVERT: A 505 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8854 (mt-10) REVERT: A 516 GLN cc_start: 0.9452 (mt0) cc_final: 0.8881 (tp-100) REVERT: A 573 SER cc_start: 0.9425 (p) cc_final: 0.8918 (p) REVERT: A 584 ILE cc_start: 0.9479 (pt) cc_final: 0.9269 (pt) REVERT: A 598 MET cc_start: 0.8911 (mtm) cc_final: 0.8559 (ttm) REVERT: A 599 GLU cc_start: 0.8536 (mp0) cc_final: 0.8133 (mp0) REVERT: A 639 ASP cc_start: 0.9063 (m-30) cc_final: 0.8627 (m-30) REVERT: A 643 THR cc_start: 0.9616 (p) cc_final: 0.9139 (t) REVERT: A 650 GLN cc_start: 0.8543 (mt0) cc_final: 0.7919 (mt0) REVERT: A 664 THR cc_start: 0.9345 (p) cc_final: 0.8625 (p) REVERT: A 667 LEU cc_start: 0.9541 (tt) cc_final: 0.9299 (tt) REVERT: A 668 ASN cc_start: 0.9328 (m110) cc_final: 0.9017 (m110) REVERT: B 17 MET cc_start: 0.8972 (mtt) cc_final: 0.8567 (mtt) REVERT: B 58 LEU cc_start: 0.9656 (mt) cc_final: 0.9432 (mt) REVERT: B 87 LYS cc_start: 0.9355 (tptp) cc_final: 0.9008 (tptp) REVERT: B 107 LYS cc_start: 0.9132 (mttt) cc_final: 0.8857 (mptt) REVERT: B 117 ARG cc_start: 0.8963 (ttm110) cc_final: 0.8639 (ttm110) REVERT: B 120 ASP cc_start: 0.8785 (m-30) cc_final: 0.8561 (m-30) REVERT: B 147 GLN cc_start: 0.9208 (mt0) cc_final: 0.8831 (mt0) REVERT: B 149 TYR cc_start: 0.9265 (t80) cc_final: 0.8733 (t80) REVERT: B 166 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8654 (mm-30) REVERT: B 172 LEU cc_start: 0.9425 (mp) cc_final: 0.8995 (mp) REVERT: B 191 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8351 (mm-40) REVERT: B 200 SER cc_start: 0.9272 (t) cc_final: 0.9065 (t) REVERT: B 211 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 227 MET cc_start: 0.9199 (mtt) cc_final: 0.8749 (mtt) REVERT: B 228 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8572 (mmtt) REVERT: B 232 ASN cc_start: 0.8980 (t160) cc_final: 0.8519 (t0) REVERT: B 257 ASP cc_start: 0.9028 (m-30) cc_final: 0.8660 (m-30) REVERT: B 278 LEU cc_start: 0.9309 (tp) cc_final: 0.9061 (tp) REVERT: B 279 SER cc_start: 0.8353 (m) cc_final: 0.7727 (p) REVERT: B 286 ASP cc_start: 0.8695 (m-30) cc_final: 0.8313 (m-30) REVERT: B 319 MET cc_start: 0.9289 (tpp) cc_final: 0.8764 (tpp) REVERT: B 322 MET cc_start: 0.9107 (mmm) cc_final: 0.8233 (mmm) REVERT: B 333 LYS cc_start: 0.9243 (tptp) cc_final: 0.8836 (tttm) REVERT: B 348 MET cc_start: 0.9392 (ptp) cc_final: 0.9083 (ptp) REVERT: B 350 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7310 (mmm160) REVERT: B 398 ASP cc_start: 0.8765 (t0) cc_final: 0.8543 (t0) REVERT: B 407 ILE cc_start: 0.9494 (mt) cc_final: 0.9034 (mt) REVERT: B 415 ASN cc_start: 0.9635 (t0) cc_final: 0.9204 (t0) REVERT: B 427 LYS cc_start: 0.9485 (tppt) cc_final: 0.9261 (mmmm) REVERT: B 458 MET cc_start: 0.9491 (mmm) cc_final: 0.8960 (mmp) REVERT: B 459 LYS cc_start: 0.9230 (mttm) cc_final: 0.8401 (mtmt) REVERT: B 474 GLN cc_start: 0.8764 (mm110) cc_final: 0.8527 (mm-40) REVERT: B 493 MET cc_start: 0.9476 (tmm) cc_final: 0.9152 (tmm) REVERT: B 505 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 561 LEU cc_start: 0.9606 (tp) cc_final: 0.9400 (tp) REVERT: B 588 GLN cc_start: 0.9418 (mm-40) cc_final: 0.9141 (mm-40) REVERT: B 595 MET cc_start: 0.9411 (mmt) cc_final: 0.9152 (mmt) REVERT: B 599 GLU cc_start: 0.8790 (pt0) cc_final: 0.8533 (pt0) REVERT: B 604 ARG cc_start: 0.9414 (tpp80) cc_final: 0.8981 (ttm-80) REVERT: B 612 TYR cc_start: 0.8560 (m-10) cc_final: 0.7931 (m-10) REVERT: B 628 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B 667 LEU cc_start: 0.9415 (tp) cc_final: 0.8819 (tp) REVERT: C 16 ASP cc_start: 0.5972 (p0) cc_final: 0.5374 (p0) REVERT: C 179 TYR cc_start: 0.8632 (t80) cc_final: 0.8369 (t80) REVERT: D 56 MET cc_start: 0.6911 (mmp) cc_final: 0.6676 (mmm) REVERT: D 59 LEU cc_start: 0.7741 (mt) cc_final: 0.7333 (pp) REVERT: D 69 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 112 LEU cc_start: 0.6330 (mm) cc_final: 0.6108 (mm) REVERT: D 137 MET cc_start: 0.5325 (mmm) cc_final: 0.4985 (mpp) REVERT: D 178 PHE cc_start: 0.9153 (m-80) cc_final: 0.8780 (m-80) REVERT: D 233 ASN cc_start: 0.8699 (m110) cc_final: 0.8317 (m110) REVERT: D 252 LEU cc_start: 0.8909 (mt) cc_final: 0.8535 (mp) REVERT: D 316 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8590 (tmmt) outliers start: 2 outliers final: 1 residues processed: 704 average time/residue: 0.3099 time to fit residues: 325.2871 Evaluate side-chains 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 617 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 232 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097066 restraints weight = 38906.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100525 restraints weight = 20641.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102837 restraints weight = 13061.605| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16386 Z= 0.127 Angle : 0.580 9.521 22134 Z= 0.308 Chirality : 0.042 0.359 2360 Planarity : 0.003 0.038 2818 Dihedral : 10.573 161.641 2242 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % 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: 0.86 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1138 sheet: -0.06 (0.41), residues: 148 loop : 0.03 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 9 HIS 0.006 0.001 HIS B 438 PHE 0.028 0.002 PHE C 168 TYR 0.025 0.001 TYR D 130 ARG 0.006 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 871) hydrogen bonds : angle 4.76672 ( 2571) covalent geometry : bond 0.00280 (16386) covalent geometry : angle 0.58016 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 694 time to evaluate : 1.700 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: A 41 ILE cc_start: 0.9587 (mm) cc_final: 0.9231 (mm) REVERT: A 54 LYS cc_start: 0.9725 (ttmm) cc_final: 0.9341 (ttmm) REVERT: A 64 TYR cc_start: 0.8900 (m-10) cc_final: 0.8683 (m-10) REVERT: A 87 LYS cc_start: 0.9501 (tptt) cc_final: 0.9273 (mmmm) REVERT: A 106 LEU cc_start: 0.9502 (tp) cc_final: 0.9110 (tp) REVERT: A 107 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8677 (mtpp) REVERT: A 118 TYR cc_start: 0.9233 (t80) cc_final: 0.8870 (t80) REVERT: A 120 ASP cc_start: 0.9022 (m-30) cc_final: 0.8767 (m-30) REVERT: A 142 ASN cc_start: 0.9404 (m-40) cc_final: 0.9105 (m110) REVERT: A 150 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 175 VAL cc_start: 0.9474 (t) cc_final: 0.9246 (t) REVERT: A 214 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8884 (mmmt) REVERT: A 223 VAL cc_start: 0.9546 (m) cc_final: 0.9202 (p) REVERT: A 227 MET cc_start: 0.9342 (mtp) cc_final: 0.8874 (mtp) REVERT: A 228 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9165 (tppp) REVERT: A 251 LEU cc_start: 0.9696 (tp) cc_final: 0.9354 (tp) REVERT: A 286 ASP cc_start: 0.8684 (m-30) cc_final: 0.8416 (m-30) REVERT: A 290 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 291 LEU cc_start: 0.9368 (mp) cc_final: 0.8854 (mt) REVERT: A 301 PHE cc_start: 0.9276 (m-80) cc_final: 0.9068 (m-10) REVERT: A 322 MET cc_start: 0.9011 (mmp) cc_final: 0.8014 (mmm) REVERT: A 345 LYS cc_start: 0.9422 (tttt) cc_final: 0.9190 (tttt) REVERT: A 348 MET cc_start: 0.9074 (ptp) cc_final: 0.8861 (ptp) REVERT: A 349 LEU cc_start: 0.9577 (mt) cc_final: 0.9239 (mt) REVERT: A 361 GLN cc_start: 0.8951 (tp40) cc_final: 0.8025 (tp-100) REVERT: A 362 ASP cc_start: 0.8170 (m-30) cc_final: 0.7589 (m-30) REVERT: A 365 ASN cc_start: 0.9099 (m110) cc_final: 0.7924 (m-40) REVERT: A 403 ILE cc_start: 0.9193 (mm) cc_final: 0.8894 (mm) REVERT: A 405 LEU cc_start: 0.9297 (mt) cc_final: 0.9093 (mt) REVERT: A 407 ILE cc_start: 0.9333 (mt) cc_final: 0.9035 (mt) REVERT: A 421 GLU cc_start: 0.8221 (pp20) cc_final: 0.8018 (pp20) REVERT: A 505 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8855 (mt-10) REVERT: A 598 MET cc_start: 0.8959 (mtm) cc_final: 0.8668 (ttm) REVERT: A 632 MET cc_start: 0.8810 (mtm) cc_final: 0.8499 (mtp) REVERT: A 634 MET cc_start: 0.9297 (mmm) cc_final: 0.8891 (mmm) REVERT: A 639 ASP cc_start: 0.9136 (m-30) cc_final: 0.8912 (m-30) REVERT: A 643 THR cc_start: 0.9588 (p) cc_final: 0.9177 (t) REVERT: A 645 GLN cc_start: 0.9277 (tp40) cc_final: 0.8890 (tp40) REVERT: A 650 GLN cc_start: 0.8678 (mt0) cc_final: 0.8034 (mt0) REVERT: A 664 THR cc_start: 0.9328 (p) cc_final: 0.8604 (p) REVERT: A 667 LEU cc_start: 0.9556 (tt) cc_final: 0.9319 (tt) REVERT: A 668 ASN cc_start: 0.9259 (m110) cc_final: 0.8873 (m110) REVERT: A 686 ARG cc_start: 0.8728 (mmt180) cc_final: 0.8130 (mmt-90) REVERT: B 18 ILE cc_start: 0.9501 (mp) cc_final: 0.9288 (mp) REVERT: B 25 GLN cc_start: 0.9238 (mt0) cc_final: 0.8596 (mt0) REVERT: B 31 GLU cc_start: 0.9027 (mp0) cc_final: 0.8766 (mt-10) REVERT: B 58 LEU cc_start: 0.9671 (mt) cc_final: 0.9445 (mt) REVERT: B 67 GLU cc_start: 0.9265 (mp0) cc_final: 0.9055 (pm20) REVERT: B 87 LYS cc_start: 0.9365 (tptp) cc_final: 0.9028 (tptp) REVERT: B 107 LYS cc_start: 0.9147 (mttt) cc_final: 0.8900 (mptt) REVERT: B 117 ARG cc_start: 0.8940 (ttm110) cc_final: 0.8736 (mmm-85) REVERT: B 118 TYR cc_start: 0.9311 (t80) cc_final: 0.9103 (t80) REVERT: B 120 ASP cc_start: 0.8764 (m-30) cc_final: 0.8391 (m-30) REVERT: B 147 GLN cc_start: 0.9201 (mt0) cc_final: 0.8935 (mt0) REVERT: B 149 TYR cc_start: 0.9301 (t80) cc_final: 0.8613 (t80) REVERT: B 172 LEU cc_start: 0.9403 (mp) cc_final: 0.9033 (mp) REVERT: B 193 SER cc_start: 0.9334 (m) cc_final: 0.9048 (p) REVERT: B 227 MET cc_start: 0.9215 (mtt) cc_final: 0.8795 (mtt) REVERT: B 232 ASN cc_start: 0.8974 (t160) cc_final: 0.8528 (t0) REVERT: B 235 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8917 (ttm-80) REVERT: B 257 ASP cc_start: 0.9082 (m-30) cc_final: 0.8754 (m-30) REVERT: B 278 LEU cc_start: 0.9268 (tp) cc_final: 0.9063 (tp) REVERT: B 279 SER cc_start: 0.8187 (m) cc_final: 0.7523 (p) REVERT: B 286 ASP cc_start: 0.8648 (m-30) cc_final: 0.8264 (m-30) REVERT: B 312 GLN cc_start: 0.8729 (mp10) cc_final: 0.8473 (mp10) REVERT: B 322 MET cc_start: 0.9091 (mmm) cc_final: 0.8579 (tpp) REVERT: B 333 LYS cc_start: 0.9239 (tptp) cc_final: 0.9031 (tttp) REVERT: B 350 ARG cc_start: 0.7646 (mmm160) cc_final: 0.7099 (mmm160) REVERT: B 378 PHE cc_start: 0.9361 (p90) cc_final: 0.9099 (p90) REVERT: B 398 ASP cc_start: 0.8765 (t0) cc_final: 0.8499 (t0) REVERT: B 407 ILE cc_start: 0.9503 (mt) cc_final: 0.8996 (mt) REVERT: B 415 ASN cc_start: 0.9632 (t0) cc_final: 0.9211 (t0) REVERT: B 427 LYS cc_start: 0.9452 (tppt) cc_final: 0.9171 (mmmm) REVERT: B 447 ASN cc_start: 0.8807 (m-40) cc_final: 0.8501 (m-40) REVERT: B 458 MET cc_start: 0.9465 (mmm) cc_final: 0.9037 (mmp) REVERT: B 459 LYS cc_start: 0.9161 (mttm) cc_final: 0.8905 (mttm) REVERT: B 469 HIS cc_start: 0.9005 (t-170) cc_final: 0.8736 (t-170) REVERT: B 474 GLN cc_start: 0.8811 (mm110) cc_final: 0.8528 (mm-40) REVERT: B 493 MET cc_start: 0.9445 (tmm) cc_final: 0.9144 (tmm) REVERT: B 505 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 595 MET cc_start: 0.9343 (mmt) cc_final: 0.9141 (mmt) REVERT: B 599 GLU cc_start: 0.8786 (pt0) cc_final: 0.8507 (pt0) REVERT: B 612 TYR cc_start: 0.8704 (m-80) cc_final: 0.8051 (m-10) REVERT: B 628 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 640 MET cc_start: 0.9363 (tpp) cc_final: 0.8854 (tpp) REVERT: B 646 GLN cc_start: 0.9484 (pt0) cc_final: 0.8829 (pm20) REVERT: C 16 ASP cc_start: 0.6091 (p0) cc_final: 0.5448 (p0) REVERT: C 179 TYR cc_start: 0.8652 (t80) cc_final: 0.8356 (t80) REVERT: D 56 MET cc_start: 0.6908 (mmp) cc_final: 0.6390 (mmm) REVERT: D 59 LEU cc_start: 0.7758 (mt) cc_final: 0.7306 (pp) REVERT: D 137 MET cc_start: 0.5514 (mmm) cc_final: 0.5277 (mpp) REVERT: D 158 VAL cc_start: 0.8773 (t) cc_final: 0.7788 (t) REVERT: D 162 TYR cc_start: 0.8208 (m-10) cc_final: 0.7854 (m-10) REVERT: D 176 LEU cc_start: 0.9364 (mt) cc_final: 0.9062 (pp) REVERT: D 178 PHE cc_start: 0.9097 (m-80) cc_final: 0.8536 (m-80) REVERT: D 233 ASN cc_start: 0.8638 (m110) cc_final: 0.8423 (m-40) REVERT: D 252 LEU cc_start: 0.8876 (mt) cc_final: 0.8521 (mp) REVERT: D 285 ILE cc_start: 0.7763 (mm) cc_final: 0.7552 (mm) REVERT: D 316 LYS cc_start: 0.8804 (tmmt) cc_final: 0.8519 (tmmt) outliers start: 1 outliers final: 0 residues processed: 695 average time/residue: 0.2700 time to fit residues: 277.1250 Evaluate side-chains 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 156 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN B 387 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 91 ASN D 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094403 restraints weight = 35537.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097039 restraints weight = 20875.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098860 restraints weight = 14288.873| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 16386 Z= 0.232 Angle : 0.645 8.878 22134 Z= 0.339 Chirality : 0.043 0.216 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.783 164.992 2242 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 1.46 % Favored : 98.48 % 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: 0.80 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1146 sheet: -0.10 (0.41), residues: 144 loop : -0.04 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 44 HIS 0.005 0.001 HIS B 438 PHE 0.028 0.002 PHE C 178 TYR 0.023 0.002 TYR D 130 ARG 0.006 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 871) hydrogen bonds : angle 4.87521 ( 2571) covalent geometry : bond 0.00496 (16386) covalent geometry : angle 0.64547 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9556 (mm) cc_final: 0.9257 (mm) REVERT: A 54 LYS cc_start: 0.9713 (ttmm) cc_final: 0.9381 (ttmm) REVERT: A 107 LYS cc_start: 0.9243 (mtpp) cc_final: 0.8758 (mtpp) REVERT: A 118 TYR cc_start: 0.9248 (t80) cc_final: 0.8960 (t80) REVERT: A 120 ASP cc_start: 0.9223 (m-30) cc_final: 0.8924 (m-30) REVERT: A 142 ASN cc_start: 0.9404 (m-40) cc_final: 0.9108 (m110) REVERT: A 147 GLN cc_start: 0.9353 (mt0) cc_final: 0.8981 (mt0) REVERT: A 150 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 168 VAL cc_start: 0.9077 (t) cc_final: 0.8782 (m) REVERT: A 175 VAL cc_start: 0.9480 (t) cc_final: 0.9270 (t) REVERT: A 179 LEU cc_start: 0.9595 (tp) cc_final: 0.9383 (tp) REVERT: A 223 VAL cc_start: 0.9608 (m) cc_final: 0.9209 (p) REVERT: A 227 MET cc_start: 0.9396 (mtp) cc_final: 0.8849 (mtp) REVERT: A 251 LEU cc_start: 0.9723 (tp) cc_final: 0.9386 (tp) REVERT: A 286 ASP cc_start: 0.8632 (m-30) cc_final: 0.8334 (m-30) REVERT: A 290 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 321 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 322 MET cc_start: 0.8872 (mmp) cc_final: 0.7623 (mmm) REVERT: A 333 LYS cc_start: 0.9066 (tptp) cc_final: 0.8794 (tptp) REVERT: A 349 LEU cc_start: 0.9574 (mt) cc_final: 0.9307 (mt) REVERT: A 361 GLN cc_start: 0.8936 (tp40) cc_final: 0.8158 (tp-100) REVERT: A 362 ASP cc_start: 0.8359 (m-30) cc_final: 0.7440 (m-30) REVERT: A 365 ASN cc_start: 0.9206 (m110) cc_final: 0.8068 (m-40) REVERT: A 403 ILE cc_start: 0.9112 (mm) cc_final: 0.8856 (mm) REVERT: A 407 ILE cc_start: 0.9369 (mt) cc_final: 0.9097 (mt) REVERT: A 421 GLU cc_start: 0.8296 (pp20) cc_final: 0.8079 (pp20) REVERT: A 458 MET cc_start: 0.9288 (mmp) cc_final: 0.9080 (mmp) REVERT: A 505 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8691 (mt-10) REVERT: A 516 GLN cc_start: 0.9454 (mt0) cc_final: 0.9252 (mt0) REVERT: A 584 ILE cc_start: 0.9527 (pt) cc_final: 0.9300 (pt) REVERT: A 588 GLN cc_start: 0.9455 (tp40) cc_final: 0.9161 (tp40) REVERT: A 636 LYS cc_start: 0.9639 (mmmm) cc_final: 0.8894 (mmmm) REVERT: A 639 ASP cc_start: 0.9158 (m-30) cc_final: 0.8710 (m-30) REVERT: A 650 GLN cc_start: 0.8788 (mt0) cc_final: 0.8108 (mt0) REVERT: A 664 THR cc_start: 0.9438 (p) cc_final: 0.8709 (p) REVERT: A 667 LEU cc_start: 0.9582 (tt) cc_final: 0.9330 (tt) REVERT: A 668 ASN cc_start: 0.9375 (m110) cc_final: 0.8982 (m110) REVERT: A 686 ARG cc_start: 0.8920 (mmt180) cc_final: 0.8200 (mmt-90) REVERT: B 67 GLU cc_start: 0.9278 (mp0) cc_final: 0.9071 (pm20) REVERT: B 87 LYS cc_start: 0.9385 (tptp) cc_final: 0.9047 (tptp) REVERT: B 116 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 120 ASP cc_start: 0.8930 (m-30) cc_final: 0.8716 (m-30) REVERT: B 147 GLN cc_start: 0.9342 (mt0) cc_final: 0.9016 (mt0) REVERT: B 149 TYR cc_start: 0.9350 (t80) cc_final: 0.8832 (t80) REVERT: B 172 LEU cc_start: 0.9422 (mp) cc_final: 0.9096 (mp) REVERT: B 191 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8607 (mm-40) REVERT: B 214 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8774 (mmtt) REVERT: B 238 ASP cc_start: 0.8379 (p0) cc_final: 0.7941 (p0) REVERT: B 257 ASP cc_start: 0.8989 (m-30) cc_final: 0.8743 (m-30) REVERT: B 279 SER cc_start: 0.8414 (m) cc_final: 0.7866 (p) REVERT: B 286 ASP cc_start: 0.8727 (m-30) cc_final: 0.8455 (m-30) REVERT: B 291 LEU cc_start: 0.9800 (mm) cc_final: 0.9512 (mt) REVERT: B 319 MET cc_start: 0.9124 (tpp) cc_final: 0.8727 (tpp) REVERT: B 322 MET cc_start: 0.9032 (mmm) cc_final: 0.8262 (tpp) REVERT: B 333 LYS cc_start: 0.9379 (tptp) cc_final: 0.9066 (tttp) REVERT: B 398 ASP cc_start: 0.9063 (t0) cc_final: 0.8713 (t0) REVERT: B 413 SER cc_start: 0.9540 (m) cc_final: 0.9328 (m) REVERT: B 415 ASN cc_start: 0.9641 (t0) cc_final: 0.9184 (t0) REVERT: B 427 LYS cc_start: 0.9416 (tppt) cc_final: 0.9124 (mmmm) REVERT: B 447 ASN cc_start: 0.8996 (m-40) cc_final: 0.8271 (m-40) REVERT: B 459 LYS cc_start: 0.9265 (mttm) cc_final: 0.9065 (mttm) REVERT: B 467 ASN cc_start: 0.9320 (m-40) cc_final: 0.8991 (m-40) REVERT: B 472 LEU cc_start: 0.9713 (mt) cc_final: 0.9472 (mt) REVERT: B 474 GLN cc_start: 0.8851 (mm110) cc_final: 0.8649 (mm-40) REVERT: B 480 GLU cc_start: 0.8806 (mp0) cc_final: 0.8333 (mp0) REVERT: B 493 MET cc_start: 0.9444 (tmm) cc_final: 0.9125 (tmm) REVERT: B 501 GLN cc_start: 0.9265 (tt0) cc_final: 0.8813 (tt0) REVERT: B 505 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 588 GLN cc_start: 0.9454 (mm-40) cc_final: 0.9232 (mm-40) REVERT: B 599 GLU cc_start: 0.8723 (pt0) cc_final: 0.8458 (pt0) REVERT: B 628 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 632 MET cc_start: 0.8724 (mtp) cc_final: 0.8175 (mtp) REVERT: B 640 MET cc_start: 0.9323 (tpp) cc_final: 0.8924 (tpp) REVERT: B 646 GLN cc_start: 0.9483 (pt0) cc_final: 0.9274 (pt0) REVERT: C 16 ASP cc_start: 0.5678 (p0) cc_final: 0.5149 (p0) REVERT: C 179 TYR cc_start: 0.8698 (t80) cc_final: 0.8359 (t80) REVERT: D 112 LEU cc_start: 0.6350 (mm) cc_final: 0.6142 (mm) REVERT: D 129 LYS cc_start: 0.8915 (tptp) cc_final: 0.8705 (tmtt) REVERT: D 137 MET cc_start: 0.5974 (mmm) cc_final: 0.5662 (mtp) REVERT: D 162 TYR cc_start: 0.8367 (m-10) cc_final: 0.8043 (m-80) REVERT: D 178 PHE cc_start: 0.8653 (m-80) cc_final: 0.7927 (m-80) REVERT: D 233 ASN cc_start: 0.8778 (m110) cc_final: 0.8306 (m110) REVERT: D 252 LEU cc_start: 0.8740 (mt) cc_final: 0.8454 (mp) REVERT: D 316 LYS cc_start: 0.8724 (tmmt) cc_final: 0.8366 (tmmt) outliers start: 1 outliers final: 0 residues processed: 678 average time/residue: 0.2763 time to fit residues: 278.2715 Evaluate side-chains 606 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096451 restraints weight = 39149.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099998 restraints weight = 20560.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102247 restraints weight = 13032.463| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16386 Z= 0.145 Angle : 0.616 8.589 22134 Z= 0.325 Chirality : 0.043 0.272 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.572 160.688 2242 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % 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: 0.63 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1149 sheet: -0.14 (0.41), residues: 148 loop : -0.22 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 124 HIS 0.014 0.001 HIS C 254 PHE 0.049 0.002 PHE D 154 TYR 0.021 0.001 TYR D 55 ARG 0.006 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 871) hydrogen bonds : angle 4.82485 ( 2571) covalent geometry : bond 0.00321 (16386) covalent geometry : angle 0.61604 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 687 time to evaluate : 1.816 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 54 LYS cc_start: 0.9730 (ttmm) cc_final: 0.9383 (ttmm) REVERT: A 107 LYS cc_start: 0.9240 (mtpp) cc_final: 0.8753 (mtpp) REVERT: A 142 ASN cc_start: 0.9410 (m-40) cc_final: 0.9092 (m110) REVERT: A 147 GLN cc_start: 0.9271 (mt0) cc_final: 0.8998 (mt0) REVERT: A 150 GLN cc_start: 0.9402 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 152 SER cc_start: 0.9535 (p) cc_final: 0.9327 (p) REVERT: A 179 LEU cc_start: 0.9621 (tp) cc_final: 0.9418 (tp) REVERT: A 223 VAL cc_start: 0.9592 (m) cc_final: 0.9228 (p) REVERT: A 227 MET cc_start: 0.9391 (mtp) cc_final: 0.8883 (mtp) REVERT: A 251 LEU cc_start: 0.9687 (tp) cc_final: 0.9366 (tp) REVERT: A 286 ASP cc_start: 0.8685 (m-30) cc_final: 0.8361 (m-30) REVERT: A 291 LEU cc_start: 0.9548 (mt) cc_final: 0.9132 (mt) REVERT: A 301 PHE cc_start: 0.9328 (m-80) cc_final: 0.9086 (m-10) REVERT: A 321 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 322 MET cc_start: 0.8928 (mmp) cc_final: 0.7598 (mmm) REVERT: A 333 LYS cc_start: 0.9065 (tptp) cc_final: 0.8646 (tptt) REVERT: A 349 LEU cc_start: 0.9576 (mt) cc_final: 0.9279 (mt) REVERT: A 361 GLN cc_start: 0.8933 (tp40) cc_final: 0.8052 (tp-100) REVERT: A 362 ASP cc_start: 0.8431 (m-30) cc_final: 0.7542 (m-30) REVERT: A 365 ASN cc_start: 0.9073 (m110) cc_final: 0.7926 (m110) REVERT: A 387 GLN cc_start: 0.9086 (mt0) cc_final: 0.8779 (mt0) REVERT: A 403 ILE cc_start: 0.9222 (mm) cc_final: 0.8958 (mm) REVERT: A 407 ILE cc_start: 0.9387 (mt) cc_final: 0.9129 (mt) REVERT: A 421 GLU cc_start: 0.8234 (pp20) cc_final: 0.7971 (pp20) REVERT: A 458 MET cc_start: 0.9179 (mmp) cc_final: 0.8732 (mmp) REVERT: A 466 MET cc_start: 0.8994 (ptt) cc_final: 0.8787 (ptt) REVERT: A 505 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8829 (mt-10) REVERT: A 571 TYR cc_start: 0.9244 (t80) cc_final: 0.8534 (t80) REVERT: A 588 GLN cc_start: 0.9462 (tp40) cc_final: 0.9134 (tp40) REVERT: A 636 LYS cc_start: 0.9570 (mmmm) cc_final: 0.8908 (mmmm) REVERT: A 639 ASP cc_start: 0.9048 (m-30) cc_final: 0.8652 (m-30) REVERT: A 646 GLN cc_start: 0.9043 (pt0) cc_final: 0.8803 (pt0) REVERT: A 650 GLN cc_start: 0.8736 (mt0) cc_final: 0.8461 (mt0) REVERT: A 664 THR cc_start: 0.9366 (p) cc_final: 0.8644 (p) REVERT: A 667 LEU cc_start: 0.9606 (tt) cc_final: 0.9340 (tt) REVERT: A 668 ASN cc_start: 0.9324 (m110) cc_final: 0.8969 (m110) REVERT: A 686 ARG cc_start: 0.8790 (mmt180) cc_final: 0.8227 (mmt-90) REVERT: B 16 ILE cc_start: 0.9281 (tp) cc_final: 0.9057 (tp) REVERT: B 58 LEU cc_start: 0.9672 (mt) cc_final: 0.9436 (mt) REVERT: B 71 LEU cc_start: 0.9696 (mm) cc_final: 0.9413 (mp) REVERT: B 87 LYS cc_start: 0.9347 (tptp) cc_final: 0.9021 (tptp) REVERT: B 95 MET cc_start: 0.9309 (mmm) cc_final: 0.8975 (mmm) REVERT: B 117 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8563 (ttm110) REVERT: B 147 GLN cc_start: 0.9266 (mt0) cc_final: 0.8858 (mt0) REVERT: B 149 TYR cc_start: 0.9408 (t80) cc_final: 0.8769 (t80) REVERT: B 172 LEU cc_start: 0.9427 (mp) cc_final: 0.8895 (mp) REVERT: B 193 SER cc_start: 0.9448 (m) cc_final: 0.9210 (m) REVERT: B 227 MET cc_start: 0.9166 (mtm) cc_final: 0.8958 (mtm) REVERT: B 232 ASN cc_start: 0.8983 (t0) cc_final: 0.8477 (t0) REVERT: B 235 ARG cc_start: 0.9258 (tpp80) cc_final: 0.9008 (ttm-80) REVERT: B 257 ASP cc_start: 0.9024 (m-30) cc_final: 0.8715 (m-30) REVERT: B 274 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7338 (mpt180) REVERT: B 279 SER cc_start: 0.8263 (m) cc_final: 0.8012 (p) REVERT: B 286 ASP cc_start: 0.8736 (m-30) cc_final: 0.8516 (m-30) REVERT: B 319 MET cc_start: 0.9131 (tpp) cc_final: 0.8788 (tpp) REVERT: B 322 MET cc_start: 0.9108 (mmm) cc_final: 0.8511 (tpp) REVERT: B 333 LYS cc_start: 0.9378 (tptp) cc_final: 0.9115 (tttp) REVERT: B 350 ARG cc_start: 0.7652 (mmm160) cc_final: 0.6946 (mmm160) REVERT: B 384 GLU cc_start: 0.8708 (pm20) cc_final: 0.7924 (pm20) REVERT: B 398 ASP cc_start: 0.8707 (t0) cc_final: 0.8399 (t0) REVERT: B 407 ILE cc_start: 0.9512 (mt) cc_final: 0.9021 (mt) REVERT: B 415 ASN cc_start: 0.9619 (t0) cc_final: 0.9273 (t0) REVERT: B 426 GLU cc_start: 0.8712 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 427 LYS cc_start: 0.9407 (tppt) cc_final: 0.8790 (tppt) REVERT: B 447 ASN cc_start: 0.8817 (m-40) cc_final: 0.8361 (m-40) REVERT: B 467 ASN cc_start: 0.9365 (m-40) cc_final: 0.9103 (m-40) REVERT: B 472 LEU cc_start: 0.9717 (mt) cc_final: 0.9461 (mt) REVERT: B 474 GLN cc_start: 0.8853 (mm110) cc_final: 0.8566 (mm-40) REVERT: B 485 ARG cc_start: 0.9255 (mtm180) cc_final: 0.8724 (mtm-85) REVERT: B 493 MET cc_start: 0.9424 (tmm) cc_final: 0.9147 (tmm) REVERT: B 494 MET cc_start: 0.9505 (mmm) cc_final: 0.9171 (mmt) REVERT: B 501 GLN cc_start: 0.9368 (tt0) cc_final: 0.8909 (tt0) REVERT: B 505 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 588 GLN cc_start: 0.9413 (mm-40) cc_final: 0.8964 (mm-40) REVERT: B 595 MET cc_start: 0.9276 (mmt) cc_final: 0.9032 (mmt) REVERT: B 599 GLU cc_start: 0.8738 (pt0) cc_final: 0.8475 (pt0) REVERT: B 612 TYR cc_start: 0.8823 (m-80) cc_final: 0.8533 (m-10) REVERT: B 628 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 632 MET cc_start: 0.8892 (mtp) cc_final: 0.8238 (mtp) REVERT: B 640 MET cc_start: 0.9388 (tpp) cc_final: 0.9046 (tpp) REVERT: B 646 GLN cc_start: 0.9484 (pt0) cc_final: 0.9260 (pt0) REVERT: C 16 ASP cc_start: 0.5754 (p0) cc_final: 0.5203 (p0) REVERT: C 42 LEU cc_start: 0.8805 (pt) cc_final: 0.8594 (pt) REVERT: C 179 TYR cc_start: 0.8663 (t80) cc_final: 0.8458 (t80) REVERT: D 112 LEU cc_start: 0.6816 (mm) cc_final: 0.6376 (mm) REVERT: D 129 LYS cc_start: 0.8966 (tptp) cc_final: 0.8610 (tmtt) REVERT: D 162 TYR cc_start: 0.8222 (m-10) cc_final: 0.7894 (m-10) REVERT: D 178 PHE cc_start: 0.9007 (m-80) cc_final: 0.8635 (m-80) REVERT: D 208 LEU cc_start: 0.8989 (mt) cc_final: 0.8720 (mt) REVERT: D 231 LEU cc_start: 0.7003 (mt) cc_final: 0.6796 (mt) REVERT: D 233 ASN cc_start: 0.8824 (m110) cc_final: 0.8442 (m110) REVERT: D 316 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8470 (tmmt) outliers start: 1 outliers final: 0 residues processed: 687 average time/residue: 0.2870 time to fit residues: 291.7223 Evaluate side-chains 608 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096051 restraints weight = 39349.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099525 restraints weight = 20833.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101815 restraints weight = 13112.987| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16386 Z= 0.133 Angle : 0.620 7.690 22134 Z= 0.326 Chirality : 0.044 0.268 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.356 156.784 2242 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.56 (0.18), residues: 1932 helix: 0.89 (0.15), residues: 1157 sheet: -0.19 (0.41), residues: 148 loop : -0.30 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 9 HIS 0.007 0.001 HIS C 201 PHE 0.038 0.002 PHE D 154 TYR 0.023 0.001 TYR B 57 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 871) hydrogen bonds : angle 4.81688 ( 2571) covalent geometry : bond 0.00292 (16386) covalent geometry : angle 0.61959 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 1.740 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 15 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8460 (mt-10) REVERT: A 54 LYS cc_start: 0.9727 (ttmm) cc_final: 0.9395 (ttmm) REVERT: A 106 LEU cc_start: 0.9529 (tp) cc_final: 0.9106 (tp) REVERT: A 107 LYS cc_start: 0.9227 (mtpp) cc_final: 0.8755 (mtpp) REVERT: A 142 ASN cc_start: 0.9405 (m-40) cc_final: 0.9114 (m110) REVERT: A 147 GLN cc_start: 0.9283 (mt0) cc_final: 0.8850 (mt0) REVERT: A 150 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 152 SER cc_start: 0.9523 (p) cc_final: 0.9311 (p) REVERT: A 223 VAL cc_start: 0.9585 (m) cc_final: 0.9202 (p) REVERT: A 227 MET cc_start: 0.9391 (mtp) cc_final: 0.8895 (mtp) REVERT: A 251 LEU cc_start: 0.9704 (tp) cc_final: 0.9379 (tp) REVERT: A 277 THR cc_start: 0.8708 (p) cc_final: 0.8462 (p) REVERT: A 286 ASP cc_start: 0.8590 (m-30) cc_final: 0.8311 (m-30) REVERT: A 333 LYS cc_start: 0.9057 (tptp) cc_final: 0.8482 (tptt) REVERT: A 349 LEU cc_start: 0.9563 (mt) cc_final: 0.9246 (mt) REVERT: A 361 GLN cc_start: 0.8871 (tp40) cc_final: 0.7963 (tp-100) REVERT: A 362 ASP cc_start: 0.8377 (m-30) cc_final: 0.7529 (m-30) REVERT: A 365 ASN cc_start: 0.8940 (m110) cc_final: 0.7842 (m110) REVERT: A 387 GLN cc_start: 0.9102 (mt0) cc_final: 0.8722 (mt0) REVERT: A 403 ILE cc_start: 0.9193 (mm) cc_final: 0.8920 (mm) REVERT: A 407 ILE cc_start: 0.9378 (mt) cc_final: 0.9105 (mt) REVERT: A 417 LEU cc_start: 0.9542 (tt) cc_final: 0.9299 (tt) REVERT: A 421 GLU cc_start: 0.8192 (pp20) cc_final: 0.7985 (pp20) REVERT: A 442 THR cc_start: 0.9379 (t) cc_final: 0.9032 (p) REVERT: A 458 MET cc_start: 0.9172 (mmp) cc_final: 0.8727 (mmp) REVERT: A 505 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8696 (mt-10) REVERT: A 571 TYR cc_start: 0.9263 (t80) cc_final: 0.8560 (t80) REVERT: A 588 GLN cc_start: 0.9456 (tp40) cc_final: 0.9121 (tp40) REVERT: A 615 MET cc_start: 0.8978 (mmp) cc_final: 0.8697 (mmp) REVERT: A 636 LYS cc_start: 0.9552 (mmmm) cc_final: 0.9003 (mmmm) REVERT: A 639 ASP cc_start: 0.8925 (m-30) cc_final: 0.8603 (m-30) REVERT: A 646 GLN cc_start: 0.9034 (pt0) cc_final: 0.8689 (pt0) REVERT: A 650 GLN cc_start: 0.8597 (mt0) cc_final: 0.8306 (mt0) REVERT: A 664 THR cc_start: 0.9328 (p) cc_final: 0.8640 (p) REVERT: A 667 LEU cc_start: 0.9612 (tt) cc_final: 0.9340 (tt) REVERT: A 668 ASN cc_start: 0.9286 (m110) cc_final: 0.8978 (m110) REVERT: B 58 LEU cc_start: 0.9668 (mt) cc_final: 0.9447 (mt) REVERT: B 71 LEU cc_start: 0.9700 (mm) cc_final: 0.9432 (mp) REVERT: B 87 LYS cc_start: 0.9350 (tptp) cc_final: 0.9041 (tptp) REVERT: B 95 MET cc_start: 0.9280 (mmm) cc_final: 0.8921 (mmm) REVERT: B 117 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8548 (ttm110) REVERT: B 147 GLN cc_start: 0.9279 (mt0) cc_final: 0.8951 (mt0) REVERT: B 149 TYR cc_start: 0.9413 (t80) cc_final: 0.8655 (t80) REVERT: B 172 LEU cc_start: 0.9419 (mp) cc_final: 0.8932 (mp) REVERT: B 232 ASN cc_start: 0.9000 (t0) cc_final: 0.8473 (t0) REVERT: B 235 ARG cc_start: 0.9244 (tpp80) cc_final: 0.8979 (ttm-80) REVERT: B 257 ASP cc_start: 0.9023 (m-30) cc_final: 0.8742 (m-30) REVERT: B 274 ARG cc_start: 0.7855 (mmt-90) cc_final: 0.7402 (mpt180) REVERT: B 286 ASP cc_start: 0.8671 (m-30) cc_final: 0.8471 (m-30) REVERT: B 296 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8819 (mmmt) REVERT: B 321 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 322 MET cc_start: 0.9034 (mmm) cc_final: 0.8048 (tpp) REVERT: B 387 GLN cc_start: 0.9255 (mt0) cc_final: 0.9012 (mt0) REVERT: B 398 ASP cc_start: 0.8719 (t0) cc_final: 0.8421 (t0) REVERT: B 407 ILE cc_start: 0.9502 (mt) cc_final: 0.9006 (mt) REVERT: B 415 ASN cc_start: 0.9590 (t0) cc_final: 0.9165 (t0) REVERT: B 447 ASN cc_start: 0.8776 (m-40) cc_final: 0.8327 (m-40) REVERT: B 458 MET cc_start: 0.9156 (mmp) cc_final: 0.8714 (mmp) REVERT: B 459 LYS cc_start: 0.9235 (mttp) cc_final: 0.8689 (mtmm) REVERT: B 467 ASN cc_start: 0.9355 (m-40) cc_final: 0.9101 (m-40) REVERT: B 474 GLN cc_start: 0.8865 (mm110) cc_final: 0.8596 (mm-40) REVERT: B 485 ARG cc_start: 0.9250 (mtm180) cc_final: 0.8930 (mtm-85) REVERT: B 493 MET cc_start: 0.9403 (tmm) cc_final: 0.9142 (tmm) REVERT: B 494 MET cc_start: 0.9506 (mmm) cc_final: 0.9225 (mmt) REVERT: B 501 GLN cc_start: 0.9220 (tt0) cc_final: 0.8989 (tt0) REVERT: B 505 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 588 GLN cc_start: 0.9388 (mm-40) cc_final: 0.8908 (mm-40) REVERT: B 599 GLU cc_start: 0.8751 (pt0) cc_final: 0.8473 (pt0) REVERT: B 604 ARG cc_start: 0.9044 (ttm-80) cc_final: 0.8829 (ttm110) REVERT: B 628 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 640 MET cc_start: 0.9336 (tpp) cc_final: 0.8980 (tpp) REVERT: B 677 ARG cc_start: 0.9375 (mmm-85) cc_final: 0.8858 (mtp85) REVERT: C 42 LEU cc_start: 0.8755 (pt) cc_final: 0.8509 (pt) REVERT: C 179 TYR cc_start: 0.8704 (t80) cc_final: 0.8470 (t80) REVERT: D 59 LEU cc_start: 0.7675 (mt) cc_final: 0.7427 (pp) REVERT: D 112 LEU cc_start: 0.6911 (mm) cc_final: 0.6442 (mm) REVERT: D 162 TYR cc_start: 0.8253 (m-10) cc_final: 0.7855 (m-10) REVERT: D 178 PHE cc_start: 0.8931 (m-80) cc_final: 0.8274 (m-80) REVERT: D 208 LEU cc_start: 0.8857 (mt) cc_final: 0.8595 (mt) REVERT: D 233 ASN cc_start: 0.8692 (m110) cc_final: 0.8412 (m110) REVERT: D 276 TYR cc_start: 0.6930 (t80) cc_final: 0.6694 (t80) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.2791 time to fit residues: 281.2566 Evaluate side-chains 608 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095753 restraints weight = 39469.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099216 restraints weight = 20809.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.101435 restraints weight = 13292.557| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16386 Z= 0.153 Angle : 0.641 9.121 22134 Z= 0.337 Chirality : 0.044 0.288 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.228 151.790 2242 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.18), residues: 1932 helix: 0.91 (0.15), residues: 1159 sheet: -0.32 (0.41), residues: 144 loop : -0.31 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.008 0.001 HIS C 201 PHE 0.032 0.002 PHE D 154 TYR 0.021 0.002 TYR B 57 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 871) hydrogen bonds : angle 4.81402 ( 2571) covalent geometry : bond 0.00339 (16386) covalent geometry : angle 0.64142 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 2.379 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9216 (mmmm) REVERT: A 107 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8655 (mtpp) REVERT: A 142 ASN cc_start: 0.9370 (m-40) cc_final: 0.9101 (m110) REVERT: A 147 GLN cc_start: 0.9309 (mt0) cc_final: 0.8854 (mt0) REVERT: A 150 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8408 (tm-30) REVERT: A 223 VAL cc_start: 0.9563 (m) cc_final: 0.9200 (p) REVERT: A 227 MET cc_start: 0.9391 (mtp) cc_final: 0.8889 (mtp) REVERT: A 251 LEU cc_start: 0.9698 (tp) cc_final: 0.9360 (tp) REVERT: A 270 ASP cc_start: 0.9180 (t70) cc_final: 0.8977 (t70) REVERT: A 286 ASP cc_start: 0.8620 (m-30) cc_final: 0.8307 (m-30) REVERT: A 321 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 322 MET cc_start: 0.8952 (mmp) cc_final: 0.8119 (mmm) REVERT: A 345 LYS cc_start: 0.9417 (tttt) cc_final: 0.9185 (tttt) REVERT: A 349 LEU cc_start: 0.9555 (mt) cc_final: 0.9228 (mt) REVERT: A 361 GLN cc_start: 0.8835 (tp40) cc_final: 0.7938 (tp-100) REVERT: A 362 ASP cc_start: 0.8393 (m-30) cc_final: 0.7565 (m-30) REVERT: A 365 ASN cc_start: 0.8893 (m110) cc_final: 0.7791 (m110) REVERT: A 387 GLN cc_start: 0.9164 (mt0) cc_final: 0.8902 (mt0) REVERT: A 403 ILE cc_start: 0.9196 (mm) cc_final: 0.8933 (mm) REVERT: A 407 ILE cc_start: 0.9407 (mt) cc_final: 0.9139 (mt) REVERT: A 421 GLU cc_start: 0.8208 (pp20) cc_final: 0.8007 (pp20) REVERT: A 442 THR cc_start: 0.9377 (t) cc_final: 0.9047 (p) REVERT: A 444 ASP cc_start: 0.8819 (p0) cc_final: 0.8509 (p0) REVERT: A 458 MET cc_start: 0.9138 (mmp) cc_final: 0.8670 (mmp) REVERT: A 505 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8871 (mt-10) REVERT: A 571 TYR cc_start: 0.9256 (t80) cc_final: 0.8495 (t80) REVERT: A 573 SER cc_start: 0.9290 (p) cc_final: 0.9079 (p) REVERT: A 584 ILE cc_start: 0.9541 (pt) cc_final: 0.9320 (pt) REVERT: A 588 GLN cc_start: 0.9435 (tp40) cc_final: 0.9124 (tp40) REVERT: A 615 MET cc_start: 0.9011 (mmp) cc_final: 0.8726 (mmp) REVERT: A 636 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9171 (mmmm) REVERT: A 645 GLN cc_start: 0.9274 (tp40) cc_final: 0.8977 (tp40) REVERT: A 646 GLN cc_start: 0.8921 (pt0) cc_final: 0.8548 (pt0) REVERT: A 650 GLN cc_start: 0.8591 (mt0) cc_final: 0.8203 (mt0) REVERT: A 664 THR cc_start: 0.9375 (p) cc_final: 0.8691 (p) REVERT: A 667 LEU cc_start: 0.9619 (tt) cc_final: 0.9344 (tt) REVERT: A 668 ASN cc_start: 0.9334 (m110) cc_final: 0.8992 (m110) REVERT: B 71 LEU cc_start: 0.9699 (mm) cc_final: 0.9438 (mp) REVERT: B 79 GLU cc_start: 0.8948 (mp0) cc_final: 0.8666 (mp0) REVERT: B 87 LYS cc_start: 0.9345 (tptp) cc_final: 0.9060 (tptp) REVERT: B 95 MET cc_start: 0.9276 (mmm) cc_final: 0.8935 (mmm) REVERT: B 116 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8858 (mt-10) REVERT: B 117 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8579 (ttm110) REVERT: B 120 ASP cc_start: 0.8880 (m-30) cc_final: 0.8632 (m-30) REVERT: B 147 GLN cc_start: 0.9277 (mt0) cc_final: 0.8960 (mt0) REVERT: B 149 TYR cc_start: 0.9404 (t80) cc_final: 0.8719 (t80) REVERT: B 172 LEU cc_start: 0.9434 (mp) cc_final: 0.9060 (mp) REVERT: B 232 ASN cc_start: 0.9006 (t0) cc_final: 0.8493 (t0) REVERT: B 238 ASP cc_start: 0.8518 (p0) cc_final: 0.8099 (p0) REVERT: B 257 ASP cc_start: 0.9023 (m-30) cc_final: 0.8733 (m-30) REVERT: B 286 ASP cc_start: 0.8727 (m-30) cc_final: 0.8514 (m-30) REVERT: B 296 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8768 (mmmt) REVERT: B 321 GLU cc_start: 0.8764 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 322 MET cc_start: 0.9081 (mmm) cc_final: 0.7839 (mpp) REVERT: B 378 PHE cc_start: 0.9285 (p90) cc_final: 0.8994 (p90) REVERT: B 387 GLN cc_start: 0.9209 (mt0) cc_final: 0.8965 (mt0) REVERT: B 398 ASP cc_start: 0.8753 (t0) cc_final: 0.8509 (t0) REVERT: B 407 ILE cc_start: 0.9501 (mt) cc_final: 0.9010 (mt) REVERT: B 415 ASN cc_start: 0.9594 (t0) cc_final: 0.9238 (t0) REVERT: B 458 MET cc_start: 0.9177 (mmp) cc_final: 0.8738 (mmp) REVERT: B 459 LYS cc_start: 0.9252 (mttp) cc_final: 0.8714 (mtmm) REVERT: B 467 ASN cc_start: 0.9337 (m-40) cc_final: 0.9054 (m-40) REVERT: B 468 LEU cc_start: 0.9461 (tp) cc_final: 0.9167 (tp) REVERT: B 472 LEU cc_start: 0.9716 (mt) cc_final: 0.9425 (mt) REVERT: B 474 GLN cc_start: 0.8901 (mm110) cc_final: 0.8682 (mm-40) REVERT: B 485 ARG cc_start: 0.9284 (mtm180) cc_final: 0.8956 (mtm-85) REVERT: B 493 MET cc_start: 0.9393 (tmm) cc_final: 0.9119 (tmm) REVERT: B 501 GLN cc_start: 0.9203 (tt0) cc_final: 0.8931 (tt0) REVERT: B 505 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8445 (mt-10) REVERT: B 588 GLN cc_start: 0.9387 (mm-40) cc_final: 0.8912 (mm-40) REVERT: B 595 MET cc_start: 0.9193 (mmm) cc_final: 0.8782 (mmm) REVERT: B 599 GLU cc_start: 0.8751 (pt0) cc_final: 0.8441 (pt0) REVERT: B 601 ILE cc_start: 0.9490 (mm) cc_final: 0.9270 (mm) REVERT: B 628 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 640 MET cc_start: 0.9364 (tpp) cc_final: 0.8940 (tpp) REVERT: B 646 GLN cc_start: 0.9470 (pt0) cc_final: 0.9179 (pt0) REVERT: C 42 LEU cc_start: 0.8720 (pt) cc_final: 0.8473 (pt) REVERT: C 179 TYR cc_start: 0.8793 (t80) cc_final: 0.8556 (t80) REVERT: D 59 LEU cc_start: 0.7636 (mt) cc_final: 0.7308 (pp) REVERT: D 69 GLN cc_start: 0.7156 (pp30) cc_final: 0.6740 (pp30) REVERT: D 105 TYR cc_start: 0.8318 (m-80) cc_final: 0.8043 (m-80) REVERT: D 112 LEU cc_start: 0.7085 (mm) cc_final: 0.6607 (mm) REVERT: D 162 TYR cc_start: 0.8285 (m-10) cc_final: 0.7846 (m-10) REVERT: D 173 TYR cc_start: 0.7811 (t80) cc_final: 0.7599 (t80) REVERT: D 178 PHE cc_start: 0.8968 (m-80) cc_final: 0.8283 (m-80) REVERT: D 208 LEU cc_start: 0.8787 (mt) cc_final: 0.8520 (mt) REVERT: D 231 LEU cc_start: 0.6902 (mt) cc_final: 0.6679 (mt) REVERT: D 233 ASN cc_start: 0.8671 (m110) cc_final: 0.8379 (m110) REVERT: D 247 TYR cc_start: 0.8791 (m-10) cc_final: 0.8464 (m-10) REVERT: D 252 LEU cc_start: 0.9176 (tp) cc_final: 0.8657 (mp) REVERT: D 276 TYR cc_start: 0.6912 (t80) cc_final: 0.6672 (t80) REVERT: D 316 LYS cc_start: 0.9343 (tmtt) cc_final: 0.8914 (tmmt) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.3150 time to fit residues: 306.6855 Evaluate side-chains 590 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092639 restraints weight = 40192.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096023 restraints weight = 21362.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098191 restraints weight = 13466.567| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16386 Z= 0.202 Angle : 0.677 8.599 22134 Z= 0.356 Chirality : 0.044 0.279 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.353 152.848 2242 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.42 (0.19), residues: 1932 helix: 0.80 (0.15), residues: 1169 sheet: -0.41 (0.40), residues: 144 loop : -0.36 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 558 HIS 0.009 0.001 HIS C 201 PHE 0.030 0.002 PHE D 154 TYR 0.025 0.002 TYR B 522 ARG 0.010 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 871) hydrogen bonds : angle 4.89946 ( 2571) covalent geometry : bond 0.00437 (16386) covalent geometry : angle 0.67719 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 1.812 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: symmetry clash REVERT: A 15 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8864 (mt-10) REVERT: A 107 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8765 (mtpp) REVERT: A 120 ASP cc_start: 0.9044 (m-30) cc_final: 0.8789 (m-30) REVERT: A 142 ASN cc_start: 0.9423 (m-40) cc_final: 0.9141 (m110) REVERT: A 147 GLN cc_start: 0.9384 (mt0) cc_final: 0.8908 (mt0) REVERT: A 150 GLN cc_start: 0.9394 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 223 VAL cc_start: 0.9567 (m) cc_final: 0.9180 (p) REVERT: A 227 MET cc_start: 0.9376 (mtp) cc_final: 0.8871 (mtp) REVERT: A 251 LEU cc_start: 0.9707 (tp) cc_final: 0.9354 (tp) REVERT: A 279 SER cc_start: 0.8900 (m) cc_final: 0.8566 (t) REVERT: A 286 ASP cc_start: 0.8644 (m-30) cc_final: 0.8353 (m-30) REVERT: A 321 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 322 MET cc_start: 0.8987 (mmp) cc_final: 0.7856 (mmm) REVERT: A 333 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9153 (ttmm) REVERT: A 349 LEU cc_start: 0.9565 (mt) cc_final: 0.9316 (mt) REVERT: A 361 GLN cc_start: 0.8883 (tp40) cc_final: 0.8380 (tp-100) REVERT: A 362 ASP cc_start: 0.8438 (m-30) cc_final: 0.7736 (m-30) REVERT: A 387 GLN cc_start: 0.9180 (mt0) cc_final: 0.8904 (mt0) REVERT: A 403 ILE cc_start: 0.9191 (mm) cc_final: 0.8925 (mm) REVERT: A 405 LEU cc_start: 0.9116 (mt) cc_final: 0.8791 (mp) REVERT: A 407 ILE cc_start: 0.9389 (mt) cc_final: 0.9096 (mt) REVERT: A 442 THR cc_start: 0.9337 (t) cc_final: 0.9072 (p) REVERT: A 444 ASP cc_start: 0.8926 (p0) cc_final: 0.8394 (p0) REVERT: A 458 MET cc_start: 0.9070 (mmp) cc_final: 0.8527 (mmp) REVERT: A 466 MET cc_start: 0.9039 (ptt) cc_final: 0.8819 (ptt) REVERT: A 505 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8696 (mt-10) REVERT: A 573 SER cc_start: 0.9334 (p) cc_final: 0.9079 (p) REVERT: A 584 ILE cc_start: 0.9571 (pt) cc_final: 0.9362 (pt) REVERT: A 615 MET cc_start: 0.8994 (mmp) cc_final: 0.8727 (mmp) REVERT: A 636 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9110 (mmmm) REVERT: A 639 ASP cc_start: 0.9021 (m-30) cc_final: 0.8751 (m-30) REVERT: A 643 THR cc_start: 0.9651 (t) cc_final: 0.9402 (t) REVERT: A 646 GLN cc_start: 0.8996 (pt0) cc_final: 0.8691 (pt0) REVERT: A 650 GLN cc_start: 0.8666 (mt0) cc_final: 0.8348 (mt0) REVERT: A 664 THR cc_start: 0.9474 (p) cc_final: 0.8768 (p) REVERT: A 667 LEU cc_start: 0.9620 (tt) cc_final: 0.9345 (tt) REVERT: A 668 ASN cc_start: 0.9402 (m110) cc_final: 0.9062 (m110) REVERT: B 87 LYS cc_start: 0.9388 (tptp) cc_final: 0.9096 (tptp) REVERT: B 95 MET cc_start: 0.9278 (mmm) cc_final: 0.8913 (mmm) REVERT: B 116 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 117 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8670 (ttm110) REVERT: B 120 ASP cc_start: 0.8926 (m-30) cc_final: 0.8722 (m-30) REVERT: B 147 GLN cc_start: 0.9294 (mt0) cc_final: 0.8935 (mt0) REVERT: B 149 TYR cc_start: 0.9436 (t80) cc_final: 0.8881 (t80) REVERT: B 172 LEU cc_start: 0.9442 (mp) cc_final: 0.9109 (mp) REVERT: B 191 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8535 (mt0) REVERT: B 214 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8533 (mptt) REVERT: B 232 ASN cc_start: 0.9042 (t0) cc_final: 0.8543 (t0) REVERT: B 235 ARG cc_start: 0.9250 (tpp80) cc_final: 0.9007 (ttm-80) REVERT: B 238 ASP cc_start: 0.8542 (p0) cc_final: 0.8129 (p0) REVERT: B 257 ASP cc_start: 0.8905 (m-30) cc_final: 0.8599 (m-30) REVERT: B 258 ILE cc_start: 0.9608 (tp) cc_final: 0.9402 (tp) REVERT: B 277 THR cc_start: 0.8654 (p) cc_final: 0.8364 (p) REVERT: B 279 SER cc_start: 0.8326 (m) cc_final: 0.8112 (p) REVERT: B 286 ASP cc_start: 0.8761 (m-30) cc_final: 0.8532 (m-30) REVERT: B 312 GLN cc_start: 0.9116 (pm20) cc_final: 0.8787 (pm20) REVERT: B 321 GLU cc_start: 0.8761 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 322 MET cc_start: 0.9092 (mmm) cc_final: 0.7795 (mpp) REVERT: B 398 ASP cc_start: 0.8833 (t0) cc_final: 0.8570 (t0) REVERT: B 415 ASN cc_start: 0.9575 (t0) cc_final: 0.9232 (t0) REVERT: B 447 ASN cc_start: 0.8761 (m-40) cc_final: 0.7640 (m-40) REVERT: B 458 MET cc_start: 0.9269 (mmp) cc_final: 0.8773 (mmp) REVERT: B 459 LYS cc_start: 0.9319 (mttp) cc_final: 0.8768 (mtmm) REVERT: B 467 ASN cc_start: 0.9312 (m-40) cc_final: 0.9051 (m-40) REVERT: B 468 LEU cc_start: 0.9551 (tp) cc_final: 0.9251 (tp) REVERT: B 472 LEU cc_start: 0.9715 (mt) cc_final: 0.9407 (mt) REVERT: B 485 ARG cc_start: 0.9297 (mtm180) cc_final: 0.8706 (mtm110) REVERT: B 493 MET cc_start: 0.9246 (tmm) cc_final: 0.9005 (tmm) REVERT: B 501 GLN cc_start: 0.9237 (tt0) cc_final: 0.8939 (tt0) REVERT: B 505 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8164 (mt-10) REVERT: B 588 GLN cc_start: 0.9403 (mm-40) cc_final: 0.8957 (mm-40) REVERT: B 595 MET cc_start: 0.9222 (mmm) cc_final: 0.8848 (mmm) REVERT: B 598 MET cc_start: 0.9352 (mtm) cc_final: 0.9084 (mtm) REVERT: B 599 GLU cc_start: 0.8792 (pt0) cc_final: 0.8535 (pt0) REVERT: B 601 ILE cc_start: 0.9517 (mm) cc_final: 0.9303 (mm) REVERT: B 628 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 640 MET cc_start: 0.9353 (tpp) cc_final: 0.8930 (tpp) REVERT: B 646 GLN cc_start: 0.9446 (pt0) cc_final: 0.8830 (pm20) REVERT: C 179 TYR cc_start: 0.8785 (t80) cc_final: 0.8561 (t80) REVERT: C 214 ASN cc_start: 0.8359 (p0) cc_final: 0.7592 (p0) REVERT: D 69 GLN cc_start: 0.7673 (pp30) cc_final: 0.7181 (pp30) REVERT: D 105 TYR cc_start: 0.8378 (m-80) cc_final: 0.8069 (m-80) REVERT: D 112 LEU cc_start: 0.7184 (mm) cc_final: 0.6748 (mm) REVERT: D 162 TYR cc_start: 0.8420 (m-10) cc_final: 0.7964 (m-10) REVERT: D 173 TYR cc_start: 0.7930 (t80) cc_final: 0.7706 (t80) REVERT: D 178 PHE cc_start: 0.8978 (m-80) cc_final: 0.8340 (m-80) REVERT: D 208 LEU cc_start: 0.8648 (mt) cc_final: 0.8404 (mt) REVERT: D 233 ASN cc_start: 0.8809 (m110) cc_final: 0.8486 (m110) REVERT: D 247 TYR cc_start: 0.8866 (m-10) cc_final: 0.8516 (m-10) REVERT: D 252 LEU cc_start: 0.9247 (tp) cc_final: 0.8635 (mp) REVERT: D 316 LYS cc_start: 0.9363 (tmtt) cc_final: 0.8955 (tmmt) outliers start: 0 outliers final: 0 residues processed: 657 average time/residue: 0.2724 time to fit residues: 266.8252 Evaluate side-chains 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 180 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095205 restraints weight = 39746.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.098642 restraints weight = 20937.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100784 restraints weight = 13327.404| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16386 Z= 0.149 Angle : 0.665 7.450 22134 Z= 0.349 Chirality : 0.044 0.218 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.125 149.431 2242 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.44 (0.19), residues: 1932 helix: 0.83 (0.15), residues: 1162 sheet: -0.55 (0.40), residues: 144 loop : -0.32 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 124 HIS 0.008 0.001 HIS C 201 PHE 0.028 0.002 PHE D 154 TYR 0.021 0.002 TYR B 57 ARG 0.011 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 871) hydrogen bonds : angle 4.90863 ( 2571) covalent geometry : bond 0.00330 (16386) covalent geometry : angle 0.66519 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6913.16 seconds wall clock time: 121 minutes 9.50 seconds (7269.50 seconds total)