Starting phenix.real_space_refine on Sun Aug 24 00:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx3_44992/08_2025/9bx3_44992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx3_44992/08_2025/9bx3_44992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2025/9bx3_44992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2025/9bx3_44992_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2025/9bx3_44992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx3_44992/08_2025/9bx3_44992.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.90, per 1000 atoms: 0.24 Number of scatterers: 15954 At special positions: 0 Unit cell: (91.98, 126.728, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 588.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.553A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.705A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.872A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.792A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.273A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.950A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.961A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.778A 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: 3.574A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.175A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.737A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.94 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: 4974 1.34 - 1.46: 2945 1.46 - 1.58: 8204 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.30e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 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 8.94e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.26e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.68e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21508 2.10 - 4.19: 459 4.19 - 6.29: 34 6.29 - 8.39: 1 8.39 - 10.49: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+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 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.58 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9427 34.31 - 68.62: 331 68.62 - 102.93: 48 102.93 - 137.24: 0 137.24 - 171.55: 2 Dihedral angle restraints: 9808 sinusoidal: 4062 harmonic: 5746 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 130.13 171.55 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.75 165.94 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2126 0.093 - 0.187: 183 0.187 - 0.280: 33 0.280 - 0.374: 4 0.374 - 0.467: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+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 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+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 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11873 3.11 - 3.70: 26426 3.70 - 4.30: 41198 4.30 - 4.90: 64928 Nonbonded interactions: 144556 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.970 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.834 16299 Z= 0.724 Angle : 0.707 10.485 22004 Z= 0.453 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.550 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70728 (22004) hydrogen bonds : bond 0.16171 ( 896) hydrogen bonds : angle 6.35194 ( 2616) Misc. bond : bond 0.83355 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 0.671 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 27 ASP cc_start: 0.7477 (p0) cc_final: 0.7151 (p0) REVERT: A 35 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 200 SER cc_start: 0.8921 (t) cc_final: 0.8679 (t) REVERT: A 204 SER cc_start: 0.8532 (m) cc_final: 0.8297 (p) REVERT: A 349 LEU cc_start: 0.8108 (tp) cc_final: 0.7850 (tp) REVERT: A 359 MET cc_start: 0.7680 (ttt) cc_final: 0.7411 (ttt) REVERT: A 411 LEU cc_start: 0.8571 (mt) cc_final: 0.8292 (mt) REVERT: A 658 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 27 ASP cc_start: 0.7317 (p0) cc_final: 0.7082 (p0) REVERT: B 72 TYR cc_start: 0.7028 (m-80) cc_final: 0.6372 (m-10) REVERT: B 100 PHE cc_start: 0.8143 (t80) cc_final: 0.7863 (t80) REVERT: B 187 ASP cc_start: 0.7691 (t70) cc_final: 0.7430 (t0) REVERT: B 200 SER cc_start: 0.8916 (t) cc_final: 0.8319 (t) REVERT: B 211 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 235 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7601 (ttm-80) REVERT: B 246 SER cc_start: 0.8358 (m) cc_final: 0.7988 (p) REVERT: B 250 TYR cc_start: 0.8608 (m-80) cc_final: 0.8175 (m-80) REVERT: B 288 PHE cc_start: 0.8346 (t80) cc_final: 0.7903 (t80) REVERT: B 373 ILE cc_start: 0.8752 (mt) cc_final: 0.8165 (mt) REVERT: B 379 SER cc_start: 0.8708 (t) cc_final: 0.8091 (t) REVERT: B 415 ASN cc_start: 0.7985 (t0) cc_final: 0.7739 (t0) REVERT: B 420 MET cc_start: 0.8428 (mmm) cc_final: 0.8163 (mmm) REVERT: B 425 ILE cc_start: 0.9006 (mt) cc_final: 0.8711 (mt) REVERT: B 490 THR cc_start: 0.8636 (m) cc_final: 0.8411 (m) REVERT: B 494 MET cc_start: 0.7414 (mtp) cc_final: 0.7107 (mtp) REVERT: B 550 MET cc_start: 0.7872 (ttm) cc_final: 0.7311 (ttm) REVERT: B 558 TRP cc_start: 0.8481 (m100) cc_final: 0.8031 (m100) REVERT: B 626 TYR cc_start: 0.8053 (m-80) cc_final: 0.7768 (m-80) REVERT: C 157 MET cc_start: 0.7101 (mtt) cc_final: 0.6738 (mtp) REVERT: C 224 LEU cc_start: 0.4867 (mt) cc_final: 0.4572 (mt) REVERT: C 260 ILE cc_start: 0.6261 (pt) cc_final: 0.5525 (pt) REVERT: D 47 LEU cc_start: 0.4053 (mt) cc_final: 0.3757 (mp) REVERT: D 56 MET cc_start: 0.5125 (mmp) cc_final: 0.4713 (mtt) REVERT: D 67 THR cc_start: 0.7180 (m) cc_final: 0.6843 (m) REVERT: D 321 TYR cc_start: 0.6611 (m-80) cc_final: 0.6092 (t80) outliers start: 23 outliers final: 4 residues processed: 875 average time/residue: 0.1483 time to fit residues: 187.6807 Evaluate side-chains 606 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 600 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.2980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 14 ASN B 158 ASN B 645 GLN C 23 ASN C 25 ASN C 28 GLN C 52 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096137 restraints weight = 33659.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099765 restraints weight = 16596.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102060 restraints weight = 10002.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103490 restraints weight = 7033.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104490 restraints weight = 5527.076| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16299 Z= 0.198 Angle : 0.688 9.977 22004 Z= 0.364 Chirality : 0.044 0.184 2348 Planarity : 0.004 0.054 2812 Dihedral : 9.098 158.901 2225 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.15 % Allowed : 19.95 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 1928 helix: 1.37 (0.15), residues: 1126 sheet: 0.42 (0.41), residues: 126 loop : 0.65 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.028 0.002 TYR C 142 PHE 0.040 0.002 PHE C 168 TRP 0.018 0.002 TRP C 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00440 (16298) covalent geometry : angle 0.68814 (22004) hydrogen bonds : bond 0.04946 ( 896) hydrogen bonds : angle 5.32789 ( 2616) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 647 time to evaluate : 0.675 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 172 LEU cc_start: 0.9204 (mp) cc_final: 0.8374 (mp) REVERT: A 179 LEU cc_start: 0.9409 (tp) cc_final: 0.9163 (tp) REVERT: A 204 SER cc_start: 0.9019 (m) cc_final: 0.8808 (p) REVERT: A 218 ASN cc_start: 0.8420 (t0) cc_final: 0.8147 (t0) REVERT: A 315 ASP cc_start: 0.8013 (p0) cc_final: 0.7708 (p0) REVERT: A 316 GLU cc_start: 0.8136 (tt0) cc_final: 0.7666 (tm-30) REVERT: A 355 TYR cc_start: 0.8242 (m-80) cc_final: 0.7981 (m-10) REVERT: A 406 ASP cc_start: 0.7995 (m-30) cc_final: 0.7274 (t0) REVERT: A 485 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7701 (mtt90) REVERT: A 493 MET cc_start: 0.8891 (tmm) cc_final: 0.8593 (tmm) REVERT: A 526 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 550 MET cc_start: 0.7673 (mtp) cc_final: 0.7373 (mtp) REVERT: A 646 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: A 657 PHE cc_start: 0.8649 (m-80) cc_final: 0.8425 (m-80) REVERT: A 662 MET cc_start: 0.8364 (mmp) cc_final: 0.8026 (mmp) REVERT: B 27 ASP cc_start: 0.8713 (p0) cc_final: 0.8403 (p0) REVERT: B 28 LYS cc_start: 0.9258 (mmtm) cc_final: 0.8945 (mmmm) REVERT: B 31 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8565 (pm20) REVERT: B 109 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8693 (m110) REVERT: B 200 SER cc_start: 0.8951 (t) cc_final: 0.8239 (t) REVERT: B 232 ASN cc_start: 0.8979 (t0) cc_final: 0.8548 (m-40) REVERT: B 246 SER cc_start: 0.7686 (m) cc_final: 0.7288 (p) REVERT: B 250 TYR cc_start: 0.9255 (m-80) cc_final: 0.8047 (m-80) REVERT: B 288 PHE cc_start: 0.9304 (t80) cc_final: 0.9025 (t80) REVERT: B 290 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (pp20) REVERT: B 322 MET cc_start: 0.9220 (mmm) cc_final: 0.9018 (mmp) REVERT: B 379 SER cc_start: 0.8833 (t) cc_final: 0.7992 (t) REVERT: B 441 GLU cc_start: 0.8430 (pt0) cc_final: 0.8221 (pt0) REVERT: B 467 ASN cc_start: 0.9139 (t0) cc_final: 0.8519 (m-40) REVERT: B 480 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 590 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8134 (t) REVERT: B 591 THR cc_start: 0.9069 (p) cc_final: 0.8746 (p) REVERT: B 599 GLU cc_start: 0.8133 (pt0) cc_final: 0.7899 (pt0) REVERT: B 601 ILE cc_start: 0.9196 (mm) cc_final: 0.8466 (mm) REVERT: B 602 GLU cc_start: 0.8152 (tt0) cc_final: 0.7627 (tt0) REVERT: B 604 ARG cc_start: 0.8957 (mmp80) cc_final: 0.8193 (tpp-160) REVERT: B 627 LYS cc_start: 0.9468 (tttp) cc_final: 0.9262 (tttp) REVERT: B 628 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: B 640 MET cc_start: 0.9090 (tpp) cc_final: 0.8607 (tpp) REVERT: B 667 LEU cc_start: 0.9054 (tt) cc_final: 0.8472 (tt) REVERT: C 23 ASN cc_start: 0.8750 (t0) cc_final: 0.8226 (t0) REVERT: C 24 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: C 178 PHE cc_start: 0.8296 (m-80) cc_final: 0.7672 (m-10) REVERT: C 193 LEU cc_start: 0.8639 (mm) cc_final: 0.8036 (mt) REVERT: C 224 LEU cc_start: 0.7492 (mt) cc_final: 0.7183 (mt) REVERT: C 239 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8461 (pp20) REVERT: D 56 MET cc_start: 0.3086 (mmp) cc_final: 0.2712 (mtt) REVERT: D 116 GLU cc_start: 0.8452 (pm20) cc_final: 0.8155 (pm20) REVERT: D 131 LEU cc_start: 0.8190 (tt) cc_final: 0.7307 (tt) REVERT: D 174 TYR cc_start: 0.4218 (t80) cc_final: 0.3613 (t80) REVERT: D 189 GLU cc_start: 0.8573 (tp30) cc_final: 0.7985 (mt-10) REVERT: D 204 TYR cc_start: 0.8854 (t80) cc_final: 0.8266 (t80) REVERT: D 216 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7559 (mm110) REVERT: D 277 PHE cc_start: 0.6228 (m-10) cc_final: 0.5952 (m-10) outliers start: 54 outliers final: 23 residues processed: 671 average time/residue: 0.1409 time to fit residues: 139.0568 Evaluate side-chains 597 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 567 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS A 608 ASN A 646 GLN B 232 ASN B 370 ASN B 588 GLN B 646 GLN C 28 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.094262 restraints weight = 34332.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097772 restraints weight = 16696.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099979 restraints weight = 10037.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101412 restraints weight = 6987.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102380 restraints weight = 5426.018| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16299 Z= 0.179 Angle : 0.648 9.757 22004 Z= 0.345 Chirality : 0.043 0.166 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.813 159.388 2219 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.15 % Allowed : 21.88 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.19), residues: 1928 helix: 1.36 (0.15), residues: 1130 sheet: 0.68 (0.40), residues: 114 loop : 0.43 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 196 TYR 0.029 0.002 TYR C 22 PHE 0.052 0.002 PHE C 168 TRP 0.020 0.002 TRP C 30 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00400 (16298) covalent geometry : angle 0.64766 (22004) hydrogen bonds : bond 0.04383 ( 896) hydrogen bonds : angle 5.19278 ( 2616) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 588 time to evaluate : 0.483 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 172 LEU cc_start: 0.9253 (mp) cc_final: 0.8952 (mp) REVERT: A 218 ASN cc_start: 0.8504 (t0) cc_final: 0.8262 (t0) REVERT: A 312 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: A 317 MET cc_start: 0.9056 (mtt) cc_final: 0.8265 (mtt) REVERT: A 322 MET cc_start: 0.8364 (tpp) cc_final: 0.7834 (tpp) REVERT: A 355 TYR cc_start: 0.8344 (m-80) cc_final: 0.8134 (m-10) REVERT: A 383 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8505 (t) REVERT: A 406 ASP cc_start: 0.8030 (m-30) cc_final: 0.7597 (m-30) REVERT: A 485 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7794 (mtt90) REVERT: A 599 GLU cc_start: 0.8338 (mp0) cc_final: 0.8098 (mp0) REVERT: A 612 TYR cc_start: 0.8899 (m-80) cc_final: 0.8623 (m-80) REVERT: B 31 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: B 121 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8668 (tpt170) REVERT: B 200 SER cc_start: 0.8935 (t) cc_final: 0.8127 (t) REVERT: B 232 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8497 (m-40) REVERT: B 246 SER cc_start: 0.7562 (m) cc_final: 0.7178 (p) REVERT: B 250 TYR cc_start: 0.9240 (m-80) cc_final: 0.8052 (m-80) REVERT: B 322 MET cc_start: 0.9344 (mmm) cc_final: 0.9111 (mmt) REVERT: B 370 ASN cc_start: 0.9267 (m-40) cc_final: 0.8600 (t0) REVERT: B 379 SER cc_start: 0.8790 (t) cc_final: 0.7971 (t) REVERT: B 441 GLU cc_start: 0.8490 (pt0) cc_final: 0.8177 (pt0) REVERT: B 494 MET cc_start: 0.8949 (mtp) cc_final: 0.8735 (mtp) REVERT: B 601 ILE cc_start: 0.9221 (mm) cc_final: 0.8381 (mm) REVERT: B 604 ARG cc_start: 0.8905 (mmp80) cc_final: 0.8225 (mmp80) REVERT: B 627 LYS cc_start: 0.9429 (tttp) cc_final: 0.9193 (ttpp) REVERT: B 628 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 640 MET cc_start: 0.9092 (tpp) cc_final: 0.8556 (tpp) REVERT: C 172 PHE cc_start: 0.7748 (m-10) cc_final: 0.7445 (m-10) REVERT: C 178 PHE cc_start: 0.8231 (m-80) cc_final: 0.7613 (m-10) REVERT: C 179 TYR cc_start: 0.8398 (t80) cc_final: 0.8081 (t80) REVERT: C 218 GLU cc_start: 0.9350 (mp0) cc_final: 0.8814 (pp20) REVERT: C 239 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8427 (pp20) REVERT: D 46 TYR cc_start: 0.8660 (m-10) cc_final: 0.8253 (m-80) REVERT: D 131 LEU cc_start: 0.8293 (tt) cc_final: 0.7957 (mt) REVERT: D 174 TYR cc_start: 0.4112 (t80) cc_final: 0.3350 (t80) REVERT: D 179 TYR cc_start: 0.8000 (t80) cc_final: 0.7697 (t80) REVERT: D 204 TYR cc_start: 0.8801 (t80) cc_final: 0.8366 (t80) REVERT: D 242 TYR cc_start: 0.7691 (t80) cc_final: 0.7365 (t80) outliers start: 54 outliers final: 28 residues processed: 612 average time/residue: 0.1180 time to fit residues: 107.0517 Evaluate side-chains 570 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 536 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.131731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092213 restraints weight = 34471.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095522 restraints weight = 16950.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097560 restraints weight = 10270.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099130 restraints weight = 7292.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100069 restraints weight = 5577.051| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16299 Z= 0.216 Angle : 0.670 12.221 22004 Z= 0.352 Chirality : 0.044 0.189 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.920 158.469 2217 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.09 % Allowed : 22.99 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.19), residues: 1928 helix: 1.21 (0.15), residues: 1143 sheet: -0.40 (0.38), residues: 146 loop : 0.48 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 196 TYR 0.020 0.002 TYR C 22 PHE 0.049 0.002 PHE C 168 TRP 0.018 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00479 (16298) covalent geometry : angle 0.66965 (22004) hydrogen bonds : bond 0.04280 ( 896) hydrogen bonds : angle 5.22354 ( 2616) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 558 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.9350 (mp) cc_final: 0.9108 (mp) REVERT: A 218 ASN cc_start: 0.8633 (t0) cc_final: 0.8374 (t0) REVERT: A 301 PHE cc_start: 0.9120 (m-10) cc_final: 0.8804 (m-10) REVERT: A 312 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: A 317 MET cc_start: 0.9046 (mtm) cc_final: 0.8685 (mtt) REVERT: A 322 MET cc_start: 0.8382 (tpp) cc_final: 0.7690 (tpp) REVERT: A 355 TYR cc_start: 0.8324 (m-80) cc_final: 0.8084 (m-10) REVERT: A 383 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8604 (t) REVERT: A 485 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7670 (mtt90) REVERT: A 599 GLU cc_start: 0.8319 (mp0) cc_final: 0.7792 (mp0) REVERT: A 668 ASN cc_start: 0.8899 (m-40) cc_final: 0.8653 (m110) REVERT: A 684 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: B 116 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8121 (mp0) REVERT: B 161 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7878 (mtt180) REVERT: B 167 LEU cc_start: 0.8907 (mt) cc_final: 0.8653 (mt) REVERT: B 200 SER cc_start: 0.8941 (t) cc_final: 0.8216 (t) REVERT: B 232 ASN cc_start: 0.9049 (m-40) cc_final: 0.8564 (m-40) REVERT: B 246 SER cc_start: 0.7539 (m) cc_final: 0.7271 (p) REVERT: B 250 TYR cc_start: 0.9210 (m-80) cc_final: 0.8083 (m-80) REVERT: B 276 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8793 (mmmt) REVERT: B 379 SER cc_start: 0.8800 (t) cc_final: 0.7732 (t) REVERT: B 550 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7620 (ttm) REVERT: B 552 ILE cc_start: 0.9447 (mp) cc_final: 0.9222 (mt) REVERT: B 590 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8624 (t) REVERT: B 599 GLU cc_start: 0.7963 (pt0) cc_final: 0.7714 (pt0) REVERT: B 601 ILE cc_start: 0.9126 (mm) cc_final: 0.8722 (mm) REVERT: B 627 LYS cc_start: 0.9412 (tttp) cc_final: 0.9102 (tttp) REVERT: B 628 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: B 640 MET cc_start: 0.9062 (tpp) cc_final: 0.8658 (tpp) REVERT: B 686 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7806 (mtm-85) REVERT: C 168 PHE cc_start: 0.7745 (m-80) cc_final: 0.7472 (m-80) REVERT: C 172 PHE cc_start: 0.7815 (m-10) cc_final: 0.7463 (m-10) REVERT: C 178 PHE cc_start: 0.8267 (m-80) cc_final: 0.7638 (m-10) REVERT: C 179 TYR cc_start: 0.8431 (t80) cc_final: 0.8119 (t80) REVERT: D 18 THR cc_start: 0.6327 (p) cc_final: 0.5999 (p) REVERT: D 46 TYR cc_start: 0.8807 (m-10) cc_final: 0.8392 (m-80) REVERT: D 56 MET cc_start: 0.2276 (mmm) cc_final: 0.1860 (mpp) REVERT: D 131 LEU cc_start: 0.8308 (tt) cc_final: 0.7866 (mt) REVERT: D 164 GLU cc_start: 0.5685 (mm-30) cc_final: 0.4605 (mm-30) REVERT: D 174 TYR cc_start: 0.4283 (t80) cc_final: 0.3763 (t80) REVERT: D 204 TYR cc_start: 0.8877 (t80) cc_final: 0.8488 (t80) REVERT: D 216 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7582 (mm110) REVERT: D 242 TYR cc_start: 0.7767 (t80) cc_final: 0.7460 (t80) REVERT: D 281 ASP cc_start: 0.8023 (p0) cc_final: 0.7423 (t70) outliers start: 53 outliers final: 35 residues processed: 576 average time/residue: 0.1188 time to fit residues: 103.2336 Evaluate side-chains 556 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 515 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 189 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 608 ASN B 62 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 24 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093634 restraints weight = 34504.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097020 restraints weight = 16930.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099176 restraints weight = 10240.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100666 restraints weight = 7163.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101594 restraints weight = 5524.334| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16299 Z= 0.168 Angle : 0.641 10.573 22004 Z= 0.337 Chirality : 0.043 0.192 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.800 153.668 2217 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.33 % Allowed : 23.75 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 1928 helix: 1.16 (0.15), residues: 1138 sheet: -0.23 (0.39), residues: 134 loop : 0.33 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 196 TYR 0.024 0.001 TYR C 262 PHE 0.037 0.002 PHE C 168 TRP 0.021 0.002 TRP C 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00376 (16298) covalent geometry : angle 0.64056 (22004) hydrogen bonds : bond 0.04110 ( 896) hydrogen bonds : angle 5.17024 ( 2616) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 572 time to evaluate : 0.516 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 164 ARG cc_start: 0.7705 (ptt90) cc_final: 0.6910 (ptt90) REVERT: A 166 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 218 ASN cc_start: 0.8751 (t0) cc_final: 0.8440 (t0) REVERT: A 301 PHE cc_start: 0.9076 (m-10) cc_final: 0.8599 (m-10) REVERT: A 355 TYR cc_start: 0.8246 (m-80) cc_final: 0.8029 (m-10) REVERT: A 383 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8585 (t) REVERT: A 485 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7661 (mtt90) REVERT: A 493 MET cc_start: 0.8743 (tmm) cc_final: 0.8184 (tmm) REVERT: A 599 GLU cc_start: 0.8310 (mp0) cc_final: 0.7962 (mp0) REVERT: A 668 ASN cc_start: 0.8963 (m-40) cc_final: 0.8672 (m110) REVERT: A 684 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: B 31 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: B 89 PHE cc_start: 0.8957 (t80) cc_final: 0.8633 (t80) REVERT: B 116 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7923 (mp0) REVERT: B 200 SER cc_start: 0.8999 (t) cc_final: 0.8223 (t) REVERT: B 228 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8411 (tppt) REVERT: B 250 TYR cc_start: 0.9227 (m-80) cc_final: 0.8256 (m-80) REVERT: B 263 ASP cc_start: 0.9088 (m-30) cc_final: 0.8880 (m-30) REVERT: B 276 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8768 (mmmt) REVERT: B 379 SER cc_start: 0.8814 (t) cc_final: 0.7825 (t) REVERT: B 467 ASN cc_start: 0.9132 (t0) cc_final: 0.8527 (m-40) REVERT: B 494 MET cc_start: 0.8935 (mtp) cc_final: 0.8693 (mtp) REVERT: B 515 ASP cc_start: 0.8955 (m-30) cc_final: 0.8697 (m-30) REVERT: B 550 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7267 (mtp) REVERT: B 590 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8598 (t) REVERT: B 599 GLU cc_start: 0.7965 (pt0) cc_final: 0.7433 (pt0) REVERT: B 601 ILE cc_start: 0.9071 (mm) cc_final: 0.8599 (mm) REVERT: B 628 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: B 639 ASP cc_start: 0.8602 (m-30) cc_final: 0.7874 (m-30) REVERT: B 640 MET cc_start: 0.9049 (tpp) cc_final: 0.8675 (tpp) REVERT: B 677 ARG cc_start: 0.8993 (mmm160) cc_final: 0.8766 (mmm-85) REVERT: B 686 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7913 (mtm-85) REVERT: C 172 PHE cc_start: 0.7896 (m-10) cc_final: 0.7544 (m-10) REVERT: C 178 PHE cc_start: 0.8353 (m-10) cc_final: 0.7816 (m-10) REVERT: C 179 TYR cc_start: 0.8455 (t80) cc_final: 0.8077 (t80) REVERT: C 181 GLN cc_start: 0.8098 (mm110) cc_final: 0.7837 (mm-40) REVERT: C 218 GLU cc_start: 0.9245 (mp0) cc_final: 0.8709 (pp20) REVERT: D 18 THR cc_start: 0.6433 (p) cc_final: 0.6095 (p) REVERT: D 20 MET cc_start: 0.8457 (ppp) cc_final: 0.8208 (ppp) REVERT: D 46 TYR cc_start: 0.8815 (m-10) cc_final: 0.8391 (m-80) REVERT: D 131 LEU cc_start: 0.8307 (tt) cc_final: 0.7829 (mt) REVERT: D 174 TYR cc_start: 0.4439 (t80) cc_final: 0.3795 (t80) REVERT: D 176 LEU cc_start: 0.9383 (mt) cc_final: 0.9129 (tp) REVERT: D 204 TYR cc_start: 0.8857 (t80) cc_final: 0.8529 (t80) REVERT: D 235 LEU cc_start: 0.8991 (mt) cc_final: 0.8665 (pp) REVERT: D 242 TYR cc_start: 0.7659 (t80) cc_final: 0.7390 (t80) REVERT: D 281 ASP cc_start: 0.8044 (p0) cc_final: 0.7555 (t70) outliers start: 57 outliers final: 34 residues processed: 597 average time/residue: 0.1237 time to fit residues: 110.1254 Evaluate side-chains 555 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 515 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095197 restraints weight = 34261.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098469 restraints weight = 16852.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100648 restraints weight = 10248.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102091 restraints weight = 7118.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103029 restraints weight = 5509.712| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16299 Z= 0.157 Angle : 0.674 12.789 22004 Z= 0.348 Chirality : 0.044 0.434 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.666 150.149 2216 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.68 % Allowed : 26.72 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 1928 helix: 1.05 (0.15), residues: 1142 sheet: -0.33 (0.39), residues: 134 loop : 0.24 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 604 TYR 0.021 0.001 TYR C 262 PHE 0.044 0.002 PHE C 168 TRP 0.033 0.003 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00354 (16298) covalent geometry : angle 0.67448 (22004) hydrogen bonds : bond 0.04054 ( 896) hydrogen bonds : angle 5.14999 ( 2616) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 562 time to evaluate : 0.646 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: A 218 ASN cc_start: 0.8800 (t0) cc_final: 0.8492 (t0) REVERT: A 301 PHE cc_start: 0.9042 (m-10) cc_final: 0.8735 (m-10) REVERT: A 312 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: A 350 ARG cc_start: 0.8343 (mtp180) cc_final: 0.7947 (mtp180) REVERT: A 379 SER cc_start: 0.9272 (t) cc_final: 0.8946 (t) REVERT: A 383 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8423 (t) REVERT: A 406 ASP cc_start: 0.8058 (m-30) cc_final: 0.7725 (m-30) REVERT: A 485 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7653 (mtt90) REVERT: A 493 MET cc_start: 0.8660 (tmm) cc_final: 0.8087 (tmm) REVERT: A 599 GLU cc_start: 0.8314 (mp0) cc_final: 0.7966 (mp0) REVERT: A 684 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: B 31 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: B 200 SER cc_start: 0.8929 (t) cc_final: 0.8124 (t) REVERT: B 228 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8416 (tppt) REVERT: B 250 TYR cc_start: 0.9213 (m-80) cc_final: 0.8226 (m-80) REVERT: B 276 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8757 (mmmt) REVERT: B 344 GLU cc_start: 0.8658 (tt0) cc_final: 0.8407 (tp30) REVERT: B 379 SER cc_start: 0.8844 (t) cc_final: 0.7705 (t) REVERT: B 467 ASN cc_start: 0.9061 (t0) cc_final: 0.8479 (t0) REVERT: B 471 TYR cc_start: 0.8686 (t80) cc_final: 0.8000 (t80) REVERT: B 494 MET cc_start: 0.8951 (mtp) cc_final: 0.8737 (mtp) REVERT: B 515 ASP cc_start: 0.8939 (m-30) cc_final: 0.8680 (m-30) REVERT: B 546 LEU cc_start: 0.9213 (mm) cc_final: 0.8874 (tt) REVERT: B 589 SER cc_start: 0.9499 (t) cc_final: 0.9151 (p) REVERT: B 590 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8536 (t) REVERT: B 639 ASP cc_start: 0.8563 (m-30) cc_final: 0.7735 (m-30) REVERT: B 640 MET cc_start: 0.9110 (tpp) cc_final: 0.8734 (tpp) REVERT: B 686 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8000 (mtm-85) REVERT: C 172 PHE cc_start: 0.7877 (m-10) cc_final: 0.7513 (m-10) REVERT: C 178 PHE cc_start: 0.8390 (m-10) cc_final: 0.7825 (m-10) REVERT: C 179 TYR cc_start: 0.8485 (t80) cc_final: 0.8123 (t80) REVERT: C 181 GLN cc_start: 0.8133 (mm110) cc_final: 0.7844 (mm-40) REVERT: C 239 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8414 (pp20) REVERT: D 18 THR cc_start: 0.6389 (p) cc_final: 0.6095 (p) REVERT: D 20 MET cc_start: 0.8420 (ppp) cc_final: 0.8151 (ppp) REVERT: D 46 TYR cc_start: 0.8809 (m-10) cc_final: 0.8408 (m-80) REVERT: D 146 GLN cc_start: 0.8106 (tp40) cc_final: 0.7819 (tp40) REVERT: D 174 TYR cc_start: 0.4368 (t80) cc_final: 0.3782 (t80) REVERT: D 176 LEU cc_start: 0.9367 (mt) cc_final: 0.9144 (tp) REVERT: D 179 TYR cc_start: 0.8161 (t80) cc_final: 0.7839 (t80) REVERT: D 204 TYR cc_start: 0.8823 (t80) cc_final: 0.8524 (t80) REVERT: D 211 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8638 (tm-30) REVERT: D 234 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: D 235 LEU cc_start: 0.8977 (mt) cc_final: 0.8715 (pp) REVERT: D 281 ASP cc_start: 0.8089 (p0) cc_final: 0.7722 (t70) outliers start: 46 outliers final: 29 residues processed: 583 average time/residue: 0.1356 time to fit residues: 117.2021 Evaluate side-chains 563 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 528 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 23 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097141 restraints weight = 34548.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100565 restraints weight = 16828.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102840 restraints weight = 10169.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104281 restraints weight = 7096.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105278 restraints weight = 5509.084| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16299 Z= 0.135 Angle : 0.680 17.303 22004 Z= 0.348 Chirality : 0.044 0.489 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.429 144.301 2216 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.45 % Allowed : 27.77 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 1928 helix: 1.08 (0.15), residues: 1128 sheet: -0.31 (0.41), residues: 134 loop : 0.16 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.019 0.001 TYR C 262 PHE 0.039 0.002 PHE C 168 TRP 0.034 0.002 TRP D 124 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00304 (16298) covalent geometry : angle 0.67987 (22004) hydrogen bonds : bond 0.03953 ( 896) hydrogen bonds : angle 5.11623 ( 2616) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 553 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8465 (mp0) REVERT: A 128 PHE cc_start: 0.8858 (t80) cc_final: 0.8623 (t80) REVERT: A 166 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 218 ASN cc_start: 0.8798 (t0) cc_final: 0.8506 (t0) REVERT: A 301 PHE cc_start: 0.9027 (m-10) cc_final: 0.8757 (m-10) REVERT: A 312 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8487 (pt0) REVERT: A 350 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7872 (mtp180) REVERT: A 379 SER cc_start: 0.9289 (t) cc_final: 0.9010 (t) REVERT: A 383 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8368 (t) REVERT: A 485 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7879 (mtt90) REVERT: A 493 MET cc_start: 0.8730 (tmm) cc_final: 0.8141 (tmm) REVERT: A 550 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6215 (mtt) REVERT: A 599 GLU cc_start: 0.8328 (mp0) cc_final: 0.7792 (mp0) REVERT: A 646 GLN cc_start: 0.9089 (mt0) cc_final: 0.8801 (mt0) REVERT: A 684 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: B 28 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8423 (mmmm) REVERT: B 116 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7966 (mp0) REVERT: B 200 SER cc_start: 0.8906 (t) cc_final: 0.8184 (t) REVERT: B 207 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7179 (mtt180) REVERT: B 228 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8466 (tppt) REVERT: B 250 TYR cc_start: 0.9206 (m-80) cc_final: 0.8313 (m-80) REVERT: B 276 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8746 (mtmm) REVERT: B 290 GLU cc_start: 0.8145 (pp20) cc_final: 0.7572 (pp20) REVERT: B 362 ASP cc_start: 0.7810 (m-30) cc_final: 0.7286 (m-30) REVERT: B 379 SER cc_start: 0.8911 (t) cc_final: 0.7787 (t) REVERT: B 467 ASN cc_start: 0.8917 (t0) cc_final: 0.8340 (t0) REVERT: B 494 MET cc_start: 0.8969 (mtp) cc_final: 0.8733 (mtp) REVERT: B 515 ASP cc_start: 0.8937 (m-30) cc_final: 0.8627 (m-30) REVERT: B 590 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 640 MET cc_start: 0.9170 (tpp) cc_final: 0.8716 (tpp) REVERT: B 677 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8161 (ttm-80) REVERT: B 686 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7915 (mtm-85) REVERT: C 172 PHE cc_start: 0.7975 (m-10) cc_final: 0.7655 (m-10) REVERT: C 178 PHE cc_start: 0.8404 (m-10) cc_final: 0.7888 (m-10) REVERT: C 179 TYR cc_start: 0.8543 (t80) cc_final: 0.8167 (t80) REVERT: C 181 GLN cc_start: 0.8110 (mm110) cc_final: 0.7910 (mm-40) REVERT: C 218 GLU cc_start: 0.9109 (mp0) cc_final: 0.8683 (pp20) REVERT: D 18 THR cc_start: 0.6341 (p) cc_final: 0.6061 (p) REVERT: D 20 MET cc_start: 0.8246 (ppp) cc_final: 0.8025 (ppp) REVERT: D 46 TYR cc_start: 0.8811 (m-10) cc_final: 0.8426 (m-80) REVERT: D 95 MET cc_start: 0.8736 (tmm) cc_final: 0.8153 (tmm) REVERT: D 146 GLN cc_start: 0.8246 (tp40) cc_final: 0.7897 (tp40) REVERT: D 174 TYR cc_start: 0.4434 (t80) cc_final: 0.3914 (t80) REVERT: D 176 LEU cc_start: 0.9337 (mt) cc_final: 0.9110 (tp) REVERT: D 204 TYR cc_start: 0.8782 (t80) cc_final: 0.8507 (t80) REVERT: D 211 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8467 (tm-30) REVERT: D 235 LEU cc_start: 0.9004 (mt) cc_final: 0.8769 (pp) REVERT: D 281 ASP cc_start: 0.8134 (p0) cc_final: 0.7897 (t70) outliers start: 42 outliers final: 25 residues processed: 569 average time/residue: 0.1357 time to fit residues: 115.3777 Evaluate side-chains 558 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 527 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 646 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.094723 restraints weight = 35016.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.098045 restraints weight = 17054.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100242 restraints weight = 10323.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101567 restraints weight = 7218.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102574 restraints weight = 5668.147| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16299 Z= 0.208 Angle : 0.714 11.971 22004 Z= 0.373 Chirality : 0.045 0.209 2348 Planarity : 0.004 0.047 2812 Dihedral : 8.627 145.124 2216 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.68 % Allowed : 28.70 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 1928 helix: 1.06 (0.15), residues: 1129 sheet: -0.55 (0.40), residues: 140 loop : 0.05 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 196 TYR 0.029 0.002 TYR B 471 PHE 0.036 0.002 PHE C 168 TRP 0.037 0.003 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00471 (16298) covalent geometry : angle 0.71409 (22004) hydrogen bonds : bond 0.04070 ( 896) hydrogen bonds : angle 5.15548 ( 2616) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 520 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.9004 (t80) cc_final: 0.8695 (t80) REVERT: A 218 ASN cc_start: 0.8902 (t0) cc_final: 0.8611 (t0) REVERT: A 312 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: A 379 SER cc_start: 0.9262 (t) cc_final: 0.8950 (t) REVERT: A 383 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 406 ASP cc_start: 0.7911 (m-30) cc_final: 0.7569 (m-30) REVERT: A 485 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.7672 (mtt90) REVERT: A 493 MET cc_start: 0.8741 (tmm) cc_final: 0.8505 (tmm) REVERT: A 599 GLU cc_start: 0.8296 (mp0) cc_final: 0.7995 (mp0) REVERT: A 603 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 668 ASN cc_start: 0.9006 (m-40) cc_final: 0.8755 (m110) REVERT: A 684 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: B 95 MET cc_start: 0.9083 (tpp) cc_final: 0.8770 (tpp) REVERT: B 200 SER cc_start: 0.8913 (t) cc_final: 0.8156 (t) REVERT: B 228 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8316 (tppt) REVERT: B 250 TYR cc_start: 0.9257 (m-80) cc_final: 0.8323 (m-80) REVERT: B 276 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8810 (mtmm) REVERT: B 379 SER cc_start: 0.8865 (t) cc_final: 0.7800 (t) REVERT: B 467 ASN cc_start: 0.9013 (t0) cc_final: 0.8424 (t0) REVERT: B 515 ASP cc_start: 0.8960 (m-30) cc_final: 0.8689 (m-30) REVERT: B 590 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8565 (t) REVERT: B 599 GLU cc_start: 0.8109 (pt0) cc_final: 0.7903 (pt0) REVERT: B 640 MET cc_start: 0.9171 (tpp) cc_final: 0.8829 (tpp) REVERT: B 686 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7942 (mtm-85) REVERT: C 137 MET cc_start: 0.3590 (mmp) cc_final: 0.3338 (mmm) REVERT: C 172 PHE cc_start: 0.8014 (m-10) cc_final: 0.7689 (m-10) REVERT: C 178 PHE cc_start: 0.8383 (m-10) cc_final: 0.7871 (m-10) REVERT: C 179 TYR cc_start: 0.8615 (t80) cc_final: 0.8191 (t80) REVERT: C 181 GLN cc_start: 0.8158 (mm110) cc_final: 0.7937 (mm-40) REVERT: D 18 THR cc_start: 0.6359 (p) cc_final: 0.6150 (p) REVERT: D 20 MET cc_start: 0.8284 (ppp) cc_final: 0.8022 (ppp) REVERT: D 46 TYR cc_start: 0.8762 (m-10) cc_final: 0.8397 (m-80) REVERT: D 95 MET cc_start: 0.8857 (tmm) cc_final: 0.8342 (tmm) REVERT: D 146 GLN cc_start: 0.8232 (tp40) cc_final: 0.7910 (tp40) REVERT: D 174 TYR cc_start: 0.4775 (t80) cc_final: 0.4506 (t80) REVERT: D 176 LEU cc_start: 0.9409 (mt) cc_final: 0.9201 (tp) REVERT: D 179 TYR cc_start: 0.8302 (t80) cc_final: 0.7955 (t80) REVERT: D 204 TYR cc_start: 0.8823 (t80) cc_final: 0.8541 (t80) REVERT: D 235 LEU cc_start: 0.9040 (mt) cc_final: 0.8772 (pp) REVERT: D 287 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4619 (mp) outliers start: 46 outliers final: 33 residues processed: 538 average time/residue: 0.1284 time to fit residues: 103.5807 Evaluate side-chains 541 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 503 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 545 ASN A 647 HIS ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095805 restraints weight = 34581.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099268 restraints weight = 16992.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101495 restraints weight = 10231.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102936 restraints weight = 7163.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103778 restraints weight = 5575.063| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16299 Z= 0.156 Angle : 0.726 16.809 22004 Z= 0.371 Chirality : 0.044 0.265 2348 Planarity : 0.004 0.047 2812 Dihedral : 8.461 142.312 2216 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.10 % Allowed : 29.93 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1928 helix: 1.01 (0.15), residues: 1133 sheet: -0.64 (0.41), residues: 142 loop : 0.01 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 196 TYR 0.025 0.001 TYR C 142 PHE 0.037 0.002 PHE C 168 TRP 0.038 0.003 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00359 (16298) covalent geometry : angle 0.72590 (22004) hydrogen bonds : bond 0.04070 ( 896) hydrogen bonds : angle 5.10857 ( 2616) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 518 time to evaluate : 0.530 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 31 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8460 (mp0) REVERT: A 128 PHE cc_start: 0.8955 (t80) cc_final: 0.8698 (t80) REVERT: A 161 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7330 (mmm-85) REVERT: A 218 ASN cc_start: 0.8850 (t0) cc_final: 0.8572 (t0) REVERT: A 301 PHE cc_start: 0.9082 (m-10) cc_final: 0.8850 (m-10) REVERT: A 312 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8431 (pt0) REVERT: A 350 ARG cc_start: 0.8351 (mtp180) cc_final: 0.7947 (mtp180) REVERT: A 379 SER cc_start: 0.9244 (t) cc_final: 0.8913 (t) REVERT: A 383 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8474 (t) REVERT: A 485 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7870 (mtt90) REVERT: A 493 MET cc_start: 0.8863 (tmm) cc_final: 0.8202 (tmm) REVERT: A 599 GLU cc_start: 0.8312 (mp0) cc_final: 0.7962 (mp0) REVERT: A 603 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 668 ASN cc_start: 0.8909 (m-40) cc_final: 0.8581 (m-40) REVERT: A 683 TYR cc_start: 0.8281 (t80) cc_final: 0.7844 (t80) REVERT: A 684 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 95 MET cc_start: 0.9071 (tpp) cc_final: 0.8712 (tpp) REVERT: B 116 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8000 (mp0) REVERT: B 200 SER cc_start: 0.8896 (t) cc_final: 0.8204 (t) REVERT: B 228 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8280 (tppt) REVERT: B 232 ASN cc_start: 0.9008 (m-40) cc_final: 0.8587 (m-40) REVERT: B 250 TYR cc_start: 0.9232 (m-80) cc_final: 0.8352 (m-80) REVERT: B 286 ASP cc_start: 0.8150 (m-30) cc_final: 0.7917 (m-30) REVERT: B 379 SER cc_start: 0.8933 (t) cc_final: 0.7913 (t) REVERT: B 467 ASN cc_start: 0.8888 (t0) cc_final: 0.8309 (t0) REVERT: B 494 MET cc_start: 0.8976 (mtp) cc_final: 0.8773 (mtp) REVERT: B 515 ASP cc_start: 0.8979 (m-30) cc_final: 0.8622 (m-30) REVERT: B 590 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8488 (t) REVERT: B 599 GLU cc_start: 0.8125 (pt0) cc_final: 0.7908 (pt0) REVERT: B 640 MET cc_start: 0.9164 (tpp) cc_final: 0.8824 (tpp) REVERT: B 677 ARG cc_start: 0.8813 (mmm160) cc_final: 0.8046 (ttm-80) REVERT: B 686 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7905 (mtm-85) REVERT: C 30 TRP cc_start: 0.6684 (p-90) cc_final: 0.6196 (p-90) REVERT: C 172 PHE cc_start: 0.7992 (m-10) cc_final: 0.7689 (m-10) REVERT: C 178 PHE cc_start: 0.8439 (m-10) cc_final: 0.7963 (m-10) REVERT: C 179 TYR cc_start: 0.8622 (t80) cc_final: 0.8248 (t80) REVERT: D 20 MET cc_start: 0.8266 (ppp) cc_final: 0.8020 (ppp) REVERT: D 95 MET cc_start: 0.8894 (tmm) cc_final: 0.8375 (tmm) REVERT: D 131 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7682 (mt) REVERT: D 137 MET cc_start: 0.8417 (mmp) cc_final: 0.7733 (mtp) REVERT: D 142 TYR cc_start: 0.8122 (m-80) cc_final: 0.7867 (t80) REVERT: D 149 ASP cc_start: 0.8005 (t0) cc_final: 0.7737 (t0) REVERT: D 174 TYR cc_start: 0.4694 (t80) cc_final: 0.4411 (t80) REVERT: D 204 TYR cc_start: 0.8863 (t80) cc_final: 0.8570 (t80) REVERT: D 242 TYR cc_start: 0.7701 (t80) cc_final: 0.7145 (m-80) REVERT: D 287 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4870 (mt) outliers start: 36 outliers final: 27 residues processed: 532 average time/residue: 0.1163 time to fit residues: 91.9489 Evaluate side-chains 533 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 500 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 191 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN A 418 ASN A 646 GLN B 43 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097421 restraints weight = 34617.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100862 restraints weight = 16930.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103121 restraints weight = 10233.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104528 restraints weight = 7134.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105498 restraints weight = 5553.539| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16299 Z= 0.150 Angle : 0.754 17.936 22004 Z= 0.384 Chirality : 0.045 0.356 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.363 139.490 2216 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.04 % Allowed : 30.40 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 1928 helix: 0.95 (0.15), residues: 1131 sheet: -0.54 (0.43), residues: 132 loop : -0.06 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 196 TYR 0.034 0.001 TYR C 142 PHE 0.036 0.002 PHE C 168 TRP 0.035 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00346 (16298) covalent geometry : angle 0.75386 (22004) hydrogen bonds : bond 0.04071 ( 896) hydrogen bonds : angle 5.09769 ( 2616) Misc. bond : bond 0.00055 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 518 time to evaluate : 0.384 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 31 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8476 (mp0) REVERT: A 128 PHE cc_start: 0.8933 (t80) cc_final: 0.8657 (t80) REVERT: A 184 ARG cc_start: 0.8726 (tpp-160) cc_final: 0.8366 (tpp80) REVERT: A 218 ASN cc_start: 0.8816 (t0) cc_final: 0.8562 (t0) REVERT: A 301 PHE cc_start: 0.9086 (m-10) cc_final: 0.8824 (m-10) REVERT: A 312 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: A 350 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7931 (mtp180) REVERT: A 379 SER cc_start: 0.9255 (t) cc_final: 0.8919 (t) REVERT: A 383 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8465 (t) REVERT: A 385 VAL cc_start: 0.9082 (t) cc_final: 0.8705 (p) REVERT: A 485 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7835 (mtt90) REVERT: A 599 GLU cc_start: 0.8312 (mp0) cc_final: 0.7963 (mp0) REVERT: A 610 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8910 (ttpp) REVERT: A 668 ASN cc_start: 0.8889 (m-40) cc_final: 0.8608 (m-40) REVERT: A 683 TYR cc_start: 0.8187 (t80) cc_final: 0.7874 (t80) REVERT: A 684 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: B 95 MET cc_start: 0.9063 (tpp) cc_final: 0.8703 (tpp) REVERT: B 116 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8120 (mp0) REVERT: B 200 SER cc_start: 0.8907 (t) cc_final: 0.8251 (t) REVERT: B 228 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8266 (mmtt) REVERT: B 250 TYR cc_start: 0.9216 (m-80) cc_final: 0.8346 (m-80) REVERT: B 259 ASN cc_start: 0.9036 (m-40) cc_final: 0.8591 (m-40) REVERT: B 286 ASP cc_start: 0.8268 (m-30) cc_final: 0.7898 (m-30) REVERT: B 288 PHE cc_start: 0.8919 (t80) cc_final: 0.8717 (t80) REVERT: B 379 SER cc_start: 0.8926 (t) cc_final: 0.7849 (t) REVERT: B 456 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8871 (ttpt) REVERT: B 494 MET cc_start: 0.8963 (mtp) cc_final: 0.8731 (mtp) REVERT: B 515 ASP cc_start: 0.8938 (m-30) cc_final: 0.8580 (m-30) REVERT: B 590 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8548 (t) REVERT: B 639 ASP cc_start: 0.8611 (m-30) cc_final: 0.7738 (m-30) REVERT: B 640 MET cc_start: 0.9151 (tpp) cc_final: 0.8818 (tpp) REVERT: B 646 GLN cc_start: 0.9137 (pt0) cc_final: 0.8506 (pm20) REVERT: B 677 ARG cc_start: 0.8803 (mmm160) cc_final: 0.8458 (mmm-85) REVERT: B 686 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7958 (mtm-85) REVERT: C 30 TRP cc_start: 0.6715 (p-90) cc_final: 0.6329 (p-90) REVERT: C 172 PHE cc_start: 0.7948 (m-10) cc_final: 0.7669 (m-10) REVERT: C 178 PHE cc_start: 0.8366 (m-10) cc_final: 0.7943 (m-10) REVERT: C 179 TYR cc_start: 0.8666 (t80) cc_final: 0.8278 (t80) REVERT: C 196 ARG cc_start: 0.7326 (tpt90) cc_final: 0.6618 (ptm-80) REVERT: C 241 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8397 (mm-30) REVERT: D 20 MET cc_start: 0.8218 (ppp) cc_final: 0.7979 (ppp) REVERT: D 137 MET cc_start: 0.8479 (mmp) cc_final: 0.7847 (mtp) REVERT: D 142 TYR cc_start: 0.8045 (m-80) cc_final: 0.7737 (t80) REVERT: D 174 TYR cc_start: 0.4772 (t80) cc_final: 0.4290 (t80) REVERT: D 204 TYR cc_start: 0.8745 (t80) cc_final: 0.8527 (t80) REVERT: D 266 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8143 (mmmt) REVERT: D 269 MET cc_start: 0.9238 (ptp) cc_final: 0.8959 (ppp) REVERT: D 287 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4576 (mp) outliers start: 35 outliers final: 27 residues processed: 532 average time/residue: 0.1059 time to fit residues: 83.9666 Evaluate side-chains 523 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 490 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 80 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: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097093 restraints weight = 34561.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100475 restraints weight = 17091.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102740 restraints weight = 10372.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104200 restraints weight = 7231.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105175 restraints weight = 5613.941| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16299 Z= 0.159 Angle : 0.752 17.784 22004 Z= 0.385 Chirality : 0.044 0.329 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.332 137.132 2216 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.04 % Allowed : 30.92 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 1928 helix: 0.94 (0.15), residues: 1131 sheet: -0.60 (0.43), residues: 132 loop : -0.01 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 196 TYR 0.023 0.001 TYR B 471 PHE 0.035 0.002 PHE C 168 TRP 0.031 0.002 TRP C 30 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00365 (16298) covalent geometry : angle 0.75164 (22004) hydrogen bonds : bond 0.04128 ( 896) hydrogen bonds : angle 5.11521 ( 2616) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.31 seconds wall clock time: 57 minutes 2.72 seconds (3422.72 seconds total)