Starting phenix.real_space_refine on Sat May 17 15:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx8_44999/05_2025/9bx8_44999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx8_44999/05_2025/9bx8_44999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx8_44999/05_2025/9bx8_44999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx8_44999/05_2025/9bx8_44999.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx8_44999/05_2025/9bx8_44999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx8_44999/05_2025/9bx8_44999_neut.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.46, per 1000 atoms: 0.59 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 127.75, 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: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.555A 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: 4.075A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.058A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.872A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.274A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A 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: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.574A 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: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.888A 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: 7.170A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A 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: 6.281A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 4.29 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: 5014 1.34 - 1.46: 2987 1.46 - 1.58: 8122 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+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 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.031 1.08e-02 8.57e+03 8.31e+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 7.53e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.76e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21502 2.10 - 4.19: 465 4.19 - 6.29: 34 6.29 - 8.38: 1 8.38 - 10.48: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -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 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 9428 34.32 - 68.64: 331 68.64 - 102.96: 47 102.96 - 137.29: 0 137.29 - 171.61: 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 301.68 130.08 171.61 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 301.68 135.68 166.00 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.30 12.30 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2128 0.093 - 0.186: 182 0.186 - 0.279: 31 0.279 - 0.372: 5 0.372 - 0.465: 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 5.42e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+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 5.50e-02 4.83e+00 pdb=" N PRO B 7 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11874 3.11 - 3.70: 26443 3.70 - 4.30: 41240 4.30 - 4.90: 65005 Nonbonded interactions: 144694 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 1.918 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 ... (remaining 144689 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: 1.090 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.410 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.833 16299 Z= 0.724 Angle : 0.708 10.476 22004 Z= 0.453 Chirality : 0.059 0.465 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.174 171.608 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 14.00 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.020 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16169 ( 896) hydrogen bonds : angle 6.35333 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70775 (22004) Misc. bond : bond 0.83327 ( 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 899 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 874 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7281 (p0) cc_final: 0.7071 (p0) REVERT: A 194 LYS cc_start: 0.8712 (tttt) cc_final: 0.8509 (tttp) REVERT: A 231 ASP cc_start: 0.8573 (t70) cc_final: 0.8361 (t70) REVERT: A 259 ASN cc_start: 0.7820 (m-40) cc_final: 0.7555 (m-40) REVERT: A 286 ASP cc_start: 0.7608 (m-30) cc_final: 0.6919 (m-30) REVERT: A 362 ASP cc_start: 0.6787 (m-30) cc_final: 0.6355 (m-30) REVERT: A 379 SER cc_start: 0.8842 (t) cc_final: 0.8400 (t) REVERT: A 591 THR cc_start: 0.8603 (p) cc_final: 0.8391 (m) REVERT: A 652 ILE cc_start: 0.9357 (mt) cc_final: 0.9057 (mt) REVERT: A 679 ILE cc_start: 0.9348 (mm) cc_final: 0.9120 (mm) REVERT: B 67 GLU cc_start: 0.7290 (mp0) cc_final: 0.7087 (mp0) REVERT: B 155 THR cc_start: 0.9148 (m) cc_final: 0.8846 (t) REVERT: B 177 ASP cc_start: 0.8411 (t0) cc_final: 0.8195 (t0) REVERT: B 194 LYS cc_start: 0.8972 (tttt) cc_final: 0.8725 (ttpt) REVERT: B 211 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6994 (mm-30) REVERT: B 250 TYR cc_start: 0.8678 (m-80) cc_final: 0.7887 (m-80) REVERT: B 286 ASP cc_start: 0.7187 (m-30) cc_final: 0.6392 (m-30) REVERT: B 357 TYR cc_start: 0.8718 (m-10) cc_final: 0.8351 (m-80) REVERT: B 362 ASP cc_start: 0.7219 (m-30) cc_final: 0.6432 (m-30) REVERT: B 379 SER cc_start: 0.9080 (t) cc_final: 0.8197 (t) REVERT: B 456 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8482 (ttpp) REVERT: B 598 MET cc_start: 0.7652 (mtm) cc_final: 0.7062 (mtm) REVERT: B 628 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 66 ASP cc_start: 0.5021 (m-30) cc_final: 0.4490 (m-30) REVERT: C 92 PHE cc_start: 0.7840 (t80) cc_final: 0.7524 (t80) REVERT: C 131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6461 (mt) REVERT: D 178 PHE cc_start: 0.5738 (m-80) cc_final: 0.5168 (m-80) REVERT: D 213 TYR cc_start: 0.4890 (t80) cc_final: 0.4610 (t80) REVERT: D 260 ILE cc_start: 0.7299 (mt) cc_final: 0.6409 (mp) REVERT: D 321 TYR cc_start: 0.7759 (m-80) cc_final: 0.6590 (m-80) outliers start: 25 outliers final: 4 residues processed: 882 average time/residue: 0.2923 time to fit residues: 369.8873 Evaluate side-chains 636 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 631 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 174 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 14 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 312 GLN A 370 ASN B 14 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 418 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 24 GLN C 28 GLN C 84 HIS C 107 ASN C 192 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 91 ASN D 127 GLN D 136 GLN D 233 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098356 restraints weight = 28089.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102076 restraints weight = 12240.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104367 restraints weight = 7166.486| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16299 Z= 0.193 Angle : 0.668 8.645 22004 Z= 0.355 Chirality : 0.045 0.198 2348 Planarity : 0.004 0.060 2812 Dihedral : 8.876 155.376 2222 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.62 % Allowed : 17.85 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 1928 helix: 1.43 (0.15), residues: 1124 sheet: 0.38 (0.41), residues: 136 loop : 0.64 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 124 HIS 0.023 0.001 HIS C 201 PHE 0.032 0.002 PHE B 261 TYR 0.027 0.002 TYR C 173 ARG 0.008 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 896) hydrogen bonds : angle 5.18323 ( 2616) covalent geometry : bond 0.00431 (16298) covalent geometry : angle 0.66769 (22004) Misc. bond : bond 0.00118 ( 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 715 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 653 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 107 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8163 (mttp) REVERT: A 246 SER cc_start: 0.7492 (m) cc_final: 0.6973 (p) REVERT: A 286 ASP cc_start: 0.8690 (m-30) cc_final: 0.7515 (m-30) REVERT: A 344 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 355 TYR cc_start: 0.8990 (m-80) cc_final: 0.8730 (m-80) REVERT: A 362 ASP cc_start: 0.7511 (m-30) cc_final: 0.6461 (m-30) REVERT: A 379 SER cc_start: 0.9078 (t) cc_final: 0.8863 (t) REVERT: A 535 ASP cc_start: 0.8325 (t0) cc_final: 0.7847 (t0) REVERT: A 668 ASN cc_start: 0.9303 (m-40) cc_final: 0.9085 (m110) REVERT: B 54 LYS cc_start: 0.9545 (tttp) cc_final: 0.9281 (tttt) REVERT: B 109 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8690 (m-40) REVERT: B 211 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7870 (mm-30) REVERT: B 250 TYR cc_start: 0.9350 (m-80) cc_final: 0.7930 (m-80) REVERT: B 263 ASP cc_start: 0.8880 (m-30) cc_final: 0.8492 (m-30) REVERT: B 286 ASP cc_start: 0.8146 (m-30) cc_final: 0.7152 (m-30) REVERT: B 321 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 322 MET cc_start: 0.9319 (mmm) cc_final: 0.9067 (mmt) REVERT: B 335 GLU cc_start: 0.7889 (tt0) cc_final: 0.7682 (mt-10) REVERT: B 355 TYR cc_start: 0.8838 (m-80) cc_final: 0.8461 (m-80) REVERT: B 357 TYR cc_start: 0.9119 (m-10) cc_final: 0.8661 (m-80) REVERT: B 362 ASP cc_start: 0.7923 (m-30) cc_final: 0.6750 (m-30) REVERT: B 366 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8392 (ptmt) REVERT: B 379 SER cc_start: 0.9240 (t) cc_final: 0.8477 (t) REVERT: B 402 GLU cc_start: 0.8346 (tp30) cc_final: 0.8122 (tm-30) REVERT: B 426 GLU cc_start: 0.8386 (pm20) cc_final: 0.8084 (pm20) REVERT: B 466 MET cc_start: 0.8876 (ptm) cc_final: 0.8592 (ptm) REVERT: B 475 ASN cc_start: 0.9459 (m-40) cc_final: 0.9172 (m110) REVERT: B 493 MET cc_start: 0.9481 (tmm) cc_final: 0.9170 (tmm) REVERT: B 529 ASP cc_start: 0.8372 (m-30) cc_final: 0.8168 (m-30) REVERT: B 599 GLU cc_start: 0.8327 (pm20) cc_final: 0.7834 (pm20) REVERT: B 604 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8027 (tpp80) REVERT: B 628 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7874 (mm-30) REVERT: C 21 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8238 (t80) REVERT: C 25 ASN cc_start: 0.8602 (m-40) cc_final: 0.8385 (m-40) REVERT: C 42 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7584 (pp) REVERT: C 53 ASP cc_start: 0.8412 (t0) cc_final: 0.8209 (t0) REVERT: C 92 PHE cc_start: 0.8165 (t80) cc_final: 0.7853 (t80) REVERT: C 95 MET cc_start: 0.8442 (tmm) cc_final: 0.8068 (tmm) REVERT: C 122 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8229 (m-10) REVERT: C 183 LYS cc_start: 0.8114 (pttt) cc_final: 0.7885 (pttp) REVERT: C 212 ILE cc_start: 0.9037 (mt) cc_final: 0.8772 (mm) REVERT: C 242 TYR cc_start: 0.9019 (t80) cc_final: 0.8621 (t80) REVERT: C 260 ILE cc_start: 0.8173 (pt) cc_final: 0.7652 (pt) REVERT: C 283 ASN cc_start: 0.7684 (p0) cc_final: 0.6951 (p0) REVERT: D 17 PHE cc_start: 0.5819 (m-80) cc_final: 0.5378 (m-80) REVERT: D 42 LEU cc_start: 0.8789 (tp) cc_final: 0.8500 (mp) REVERT: D 117 THR cc_start: 0.8911 (m) cc_final: 0.7863 (m) REVERT: D 137 MET cc_start: 0.4557 (mtp) cc_final: 0.4070 (mmm) REVERT: D 154 PHE cc_start: 0.9344 (t80) cc_final: 0.8766 (t80) REVERT: D 169 TYR cc_start: 0.8206 (m-80) cc_final: 0.7762 (m-80) REVERT: D 181 GLN cc_start: 0.8498 (mt0) cc_final: 0.8106 (mp10) REVERT: D 212 ILE cc_start: 0.9634 (mt) cc_final: 0.9325 (mt) REVERT: D 213 TYR cc_start: 0.8044 (t80) cc_final: 0.7655 (t80) REVERT: D 233 ASN cc_start: 0.8083 (m-40) cc_final: 0.7881 (m110) REVERT: D 242 TYR cc_start: 0.7970 (t80) cc_final: 0.7672 (t80) REVERT: D 244 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7846 (pt0) REVERT: D 287 LEU cc_start: 0.5802 (mt) cc_final: 0.5495 (mp) REVERT: D 315 LEU cc_start: 0.9153 (mt) cc_final: 0.8816 (mt) outliers start: 62 outliers final: 26 residues processed: 681 average time/residue: 0.2717 time to fit residues: 272.9007 Evaluate side-chains 604 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 573 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 186 GLN C 263 ASN C 265 ASN D 127 GLN D 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.092546 restraints weight = 28439.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096142 restraints weight = 11978.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098379 restraints weight = 6888.274| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4542 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= 0.196 Angle : 0.635 8.596 22004 Z= 0.335 Chirality : 0.043 0.170 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.730 155.606 2219 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.85 % Allowed : 20.07 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1928 helix: 1.33 (0.15), residues: 1135 sheet: 0.15 (0.40), residues: 144 loop : 0.58 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 124 HIS 0.025 0.001 HIS C 201 PHE 0.037 0.002 PHE D 172 TYR 0.041 0.002 TYR D 242 ARG 0.005 0.001 ARG B 669 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 896) hydrogen bonds : angle 5.06300 ( 2616) covalent geometry : bond 0.00449 (16298) covalent geometry : angle 0.63486 (22004) Misc. bond : bond 0.00074 ( 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 690 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 624 time to evaluate : 1.712 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 150 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8427 (tp-100) REVERT: A 275 VAL cc_start: 0.9492 (t) cc_final: 0.9275 (t) REVERT: A 286 ASP cc_start: 0.8818 (m-30) cc_final: 0.7714 (m-30) REVERT: A 344 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 355 TYR cc_start: 0.8967 (m-80) cc_final: 0.8743 (m-10) REVERT: A 362 ASP cc_start: 0.7572 (m-30) cc_final: 0.6743 (m-30) REVERT: A 379 SER cc_start: 0.9095 (t) cc_final: 0.8834 (t) REVERT: A 420 MET cc_start: 0.9278 (mmm) cc_final: 0.9061 (mmm) REVERT: A 444 ASP cc_start: 0.8458 (t0) cc_final: 0.7865 (t70) REVERT: A 446 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7833 (tpp80) REVERT: A 485 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.7849 (mtm-85) REVERT: A 604 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7432 (ttm110) REVERT: B 98 PHE cc_start: 0.9361 (t80) cc_final: 0.8836 (t80) REVERT: B 109 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: B 155 THR cc_start: 0.9533 (m) cc_final: 0.9308 (t) REVERT: B 167 LEU cc_start: 0.8936 (mt) cc_final: 0.8462 (mp) REVERT: B 174 GLU cc_start: 0.8455 (tp30) cc_final: 0.8167 (tp30) REVERT: B 202 ASN cc_start: 0.9124 (t0) cc_final: 0.8588 (t0) REVERT: B 250 TYR cc_start: 0.9370 (m-80) cc_final: 0.7654 (m-80) REVERT: B 286 ASP cc_start: 0.8295 (m-30) cc_final: 0.7416 (m-30) REVERT: B 318 ASP cc_start: 0.8488 (t0) cc_final: 0.7440 (t0) REVERT: B 334 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8686 (ptpt) REVERT: B 335 GLU cc_start: 0.8042 (tt0) cc_final: 0.7759 (mt-10) REVERT: B 355 TYR cc_start: 0.8873 (m-80) cc_final: 0.8513 (m-80) REVERT: B 357 TYR cc_start: 0.9099 (m-10) cc_final: 0.8670 (m-80) REVERT: B 362 ASP cc_start: 0.8083 (m-30) cc_final: 0.6939 (m-30) REVERT: B 379 SER cc_start: 0.9157 (t) cc_final: 0.8525 (t) REVERT: B 402 GLU cc_start: 0.8521 (tp30) cc_final: 0.8241 (tm-30) REVERT: B 493 MET cc_start: 0.9532 (tmm) cc_final: 0.9088 (tmm) REVERT: B 599 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: B 602 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 603 GLU cc_start: 0.8164 (tp30) cc_final: 0.7633 (tp30) REVERT: B 612 TYR cc_start: 0.8657 (m-80) cc_final: 0.6904 (m-80) REVERT: B 628 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7885 (mm-30) REVERT: B 668 ASN cc_start: 0.8788 (m-40) cc_final: 0.8404 (m110) REVERT: C 20 MET cc_start: 0.8110 (tpt) cc_final: 0.7695 (ptt) REVERT: C 21 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8200 (t80) REVERT: C 25 ASN cc_start: 0.8887 (m-40) cc_final: 0.8619 (m-40) REVERT: C 37 LEU cc_start: 0.6116 (mp) cc_final: 0.5295 (mt) REVERT: C 42 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7669 (pp) REVERT: C 92 PHE cc_start: 0.8303 (t80) cc_final: 0.8058 (t80) REVERT: C 95 MET cc_start: 0.8490 (tmm) cc_final: 0.8177 (tmm) REVERT: C 105 TYR cc_start: 0.7506 (m-80) cc_final: 0.7125 (m-80) REVERT: C 122 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8139 (m-10) REVERT: C 145 ILE cc_start: 0.8608 (tp) cc_final: 0.8152 (tp) REVERT: C 213 TYR cc_start: 0.7838 (t80) cc_final: 0.7608 (t80) REVERT: C 227 PHE cc_start: 0.8598 (t80) cc_final: 0.8228 (t80) REVERT: C 242 TYR cc_start: 0.9056 (t80) cc_final: 0.8607 (t80) REVERT: C 260 ILE cc_start: 0.8366 (pt) cc_final: 0.8104 (pt) REVERT: C 287 LEU cc_start: 0.1373 (OUTLIER) cc_final: 0.1044 (mp) REVERT: D 23 ASN cc_start: 0.9397 (t0) cc_final: 0.9110 (t0) REVERT: D 27 LYS cc_start: 0.8903 (mttt) cc_final: 0.8637 (pttp) REVERT: D 30 TRP cc_start: 0.8573 (p-90) cc_final: 0.8096 (p-90) REVERT: D 42 LEU cc_start: 0.8746 (tp) cc_final: 0.8313 (mp) REVERT: D 46 TYR cc_start: 0.8919 (m-10) cc_final: 0.8435 (m-10) REVERT: D 56 MET cc_start: 0.6983 (mmm) cc_final: 0.6563 (ptp) REVERT: D 137 MET cc_start: 0.5094 (mtp) cc_final: 0.4617 (mmt) REVERT: D 154 PHE cc_start: 0.9392 (t80) cc_final: 0.8820 (t80) REVERT: D 178 PHE cc_start: 0.9313 (m-80) cc_final: 0.8586 (m-80) REVERT: D 186 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8119 (mp10) REVERT: D 212 ILE cc_start: 0.9677 (mt) cc_final: 0.9412 (mt) REVERT: D 213 TYR cc_start: 0.8409 (t80) cc_final: 0.7667 (t80) REVERT: D 215 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8597 (mtmm) REVERT: D 242 TYR cc_start: 0.7861 (t80) cc_final: 0.7339 (t80) REVERT: D 244 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7939 (pt0) outliers start: 66 outliers final: 42 residues processed: 647 average time/residue: 0.2701 time to fit residues: 257.4451 Evaluate side-chains 614 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 565 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 646 GLN A 668 ASN B 131 ASN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 132 GLN D 210 GLN D 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.091620 restraints weight = 28925.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095086 restraints weight = 12372.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097267 restraints weight = 7207.587| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16299 Z= 0.219 Angle : 0.644 10.317 22004 Z= 0.339 Chirality : 0.044 0.192 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.770 152.988 2218 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.08 % Allowed : 20.71 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1928 helix: 1.29 (0.15), residues: 1141 sheet: -0.18 (0.40), residues: 152 loop : 0.49 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 124 HIS 0.025 0.002 HIS C 201 PHE 0.032 0.002 PHE D 172 TYR 0.024 0.002 TYR D 236 ARG 0.011 0.001 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 896) hydrogen bonds : angle 5.06089 ( 2616) covalent geometry : bond 0.00494 (16298) covalent geometry : angle 0.64396 (22004) Misc. bond : bond 0.00066 ( 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 671 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 601 time to evaluate : 1.943 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 150 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8487 (tp-100) REVERT: A 218 ASN cc_start: 0.8930 (t0) cc_final: 0.8478 (t0) REVERT: A 228 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8728 (mmtt) REVERT: A 266 LYS cc_start: 0.9022 (mttt) cc_final: 0.8751 (mttt) REVERT: A 286 ASP cc_start: 0.8691 (m-30) cc_final: 0.7714 (m-30) REVERT: A 344 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 362 ASP cc_start: 0.7795 (m-30) cc_final: 0.6711 (m-30) REVERT: A 379 SER cc_start: 0.9111 (t) cc_final: 0.8893 (t) REVERT: A 384 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: A 444 ASP cc_start: 0.8591 (t0) cc_final: 0.8292 (t0) REVERT: A 485 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8046 (mtm-85) REVERT: A 586 TYR cc_start: 0.9044 (m-80) cc_final: 0.8735 (m-10) REVERT: A 604 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7564 (ttm110) REVERT: A 639 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: A 684 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: B 98 PHE cc_start: 0.9370 (t80) cc_final: 0.8742 (t80) REVERT: B 109 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8616 (m-40) REVERT: B 167 LEU cc_start: 0.9063 (mt) cc_final: 0.8639 (mp) REVERT: B 250 TYR cc_start: 0.9426 (m-80) cc_final: 0.7640 (m-80) REVERT: B 263 ASP cc_start: 0.8803 (m-30) cc_final: 0.8400 (m-30) REVERT: B 286 ASP cc_start: 0.8064 (m-30) cc_final: 0.7415 (m-30) REVERT: B 318 ASP cc_start: 0.8016 (t0) cc_final: 0.7518 (t0) REVERT: B 334 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8709 (ptpt) REVERT: B 342 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9335 (tt) REVERT: B 355 TYR cc_start: 0.8794 (m-80) cc_final: 0.8526 (m-80) REVERT: B 362 ASP cc_start: 0.8055 (m-30) cc_final: 0.6901 (m-30) REVERT: B 379 SER cc_start: 0.9171 (t) cc_final: 0.8601 (t) REVERT: B 493 MET cc_start: 0.9483 (tmm) cc_final: 0.9283 (tmm) REVERT: B 586 TYR cc_start: 0.9191 (m-80) cc_final: 0.8518 (m-80) REVERT: B 599 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: B 602 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 603 GLU cc_start: 0.8242 (tp30) cc_final: 0.7771 (tp30) REVERT: B 604 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8204 (tpp80) REVERT: B 612 TYR cc_start: 0.8790 (m-80) cc_final: 0.7480 (m-80) REVERT: B 628 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7984 (mm-30) REVERT: C 20 MET cc_start: 0.8212 (tpt) cc_final: 0.7800 (ptt) REVERT: C 21 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8306 (t80) REVERT: C 40 ASP cc_start: 0.8254 (p0) cc_final: 0.7992 (p0) REVERT: C 42 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7761 (pp) REVERT: C 92 PHE cc_start: 0.8328 (t80) cc_final: 0.7936 (t80) REVERT: C 95 MET cc_start: 0.8678 (tmm) cc_final: 0.8244 (tmm) REVERT: C 122 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: C 149 ASP cc_start: 0.8561 (t0) cc_final: 0.8320 (t0) REVERT: C 178 PHE cc_start: 0.9250 (m-10) cc_final: 0.8930 (m-10) REVERT: C 183 LYS cc_start: 0.8058 (pttm) cc_final: 0.7783 (pttm) REVERT: C 227 PHE cc_start: 0.8701 (t80) cc_final: 0.8397 (t80) REVERT: C 242 TYR cc_start: 0.9049 (t80) cc_final: 0.8671 (t80) REVERT: C 287 LEU cc_start: 0.2196 (OUTLIER) cc_final: 0.1679 (mt) REVERT: D 46 TYR cc_start: 0.8988 (m-10) cc_final: 0.8712 (m-10) REVERT: D 56 MET cc_start: 0.7396 (mmm) cc_final: 0.6739 (ptp) REVERT: D 137 MET cc_start: 0.5781 (mtp) cc_final: 0.5369 (mmt) REVERT: D 154 PHE cc_start: 0.9370 (t80) cc_final: 0.8863 (t80) REVERT: D 178 PHE cc_start: 0.9320 (m-80) cc_final: 0.8727 (m-80) REVERT: D 210 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8594 (pp30) REVERT: D 213 TYR cc_start: 0.8474 (t80) cc_final: 0.7964 (t80) REVERT: D 225 ARG cc_start: 0.9188 (mtm-85) cc_final: 0.8659 (mtm180) REVERT: D 236 TYR cc_start: 0.7820 (t80) cc_final: 0.7419 (t80) REVERT: D 244 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7806 (pt0) outliers start: 70 outliers final: 36 residues processed: 633 average time/residue: 0.2758 time to fit residues: 256.3296 Evaluate side-chains 604 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 556 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 588 GLN C 107 ASN C 214 ASN C 263 ASN ** D 216 GLN ** 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 = 0.3687 r_free = 0.3687 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093912 restraints weight = 29271.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097336 restraints weight = 12331.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099439 restraints weight = 7096.411| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16299 Z= 0.175 Angle : 0.635 10.961 22004 Z= 0.332 Chirality : 0.043 0.228 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.676 150.958 2217 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.79 % Allowed : 22.58 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1928 helix: 1.22 (0.15), residues: 1147 sheet: -0.32 (0.41), residues: 152 loop : 0.43 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 124 HIS 0.026 0.001 HIS C 201 PHE 0.031 0.002 PHE D 172 TYR 0.024 0.001 TYR C 142 ARG 0.009 0.001 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 896) hydrogen bonds : angle 5.02468 ( 2616) covalent geometry : bond 0.00395 (16298) covalent geometry : angle 0.63476 (22004) Misc. bond : bond 0.00052 ( 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 646 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 581 time to evaluate : 1.716 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 49 HIS cc_start: 0.8187 (m-70) cc_final: 0.7901 (m-70) REVERT: A 218 ASN cc_start: 0.8933 (t0) cc_final: 0.8520 (t0) REVERT: A 286 ASP cc_start: 0.8696 (m-30) cc_final: 0.7801 (m-30) REVERT: A 344 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 355 TYR cc_start: 0.8905 (m-80) cc_final: 0.8457 (m-80) REVERT: A 362 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: A 379 SER cc_start: 0.9094 (t) cc_final: 0.8871 (t) REVERT: A 384 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: A 444 ASP cc_start: 0.8432 (t0) cc_final: 0.7969 (t70) REVERT: A 446 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7621 (tpp80) REVERT: A 485 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.7681 (mtm110) REVERT: A 570 MET cc_start: 0.8881 (mtp) cc_final: 0.8578 (mtp) REVERT: A 586 TYR cc_start: 0.9004 (m-80) cc_final: 0.8713 (m-10) REVERT: A 604 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7513 (ttm110) REVERT: A 639 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8187 (m-30) REVERT: A 684 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: B 98 PHE cc_start: 0.9324 (t80) cc_final: 0.8656 (t80) REVERT: B 109 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8599 (m-40) REVERT: B 167 LEU cc_start: 0.9125 (mt) cc_final: 0.8620 (mp) REVERT: B 250 TYR cc_start: 0.9413 (m-80) cc_final: 0.7600 (m-80) REVERT: B 263 ASP cc_start: 0.8818 (m-30) cc_final: 0.8421 (m-30) REVERT: B 286 ASP cc_start: 0.8117 (m-30) cc_final: 0.7333 (m-30) REVERT: B 342 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9341 (tt) REVERT: B 355 TYR cc_start: 0.8707 (m-80) cc_final: 0.8400 (m-80) REVERT: B 357 TYR cc_start: 0.9021 (m-10) cc_final: 0.8719 (m-80) REVERT: B 362 ASP cc_start: 0.8048 (m-30) cc_final: 0.6777 (m-30) REVERT: B 379 SER cc_start: 0.9212 (t) cc_final: 0.8496 (t) REVERT: B 599 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: B 603 GLU cc_start: 0.8218 (tp30) cc_final: 0.7862 (tp30) REVERT: B 610 LYS cc_start: 0.8412 (tppt) cc_final: 0.6988 (tppt) REVERT: B 612 TYR cc_start: 0.8622 (m-80) cc_final: 0.7966 (m-80) REVERT: B 628 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8006 (mm-30) REVERT: B 659 LYS cc_start: 0.8440 (mmmt) cc_final: 0.7713 (mmmt) REVERT: B 668 ASN cc_start: 0.8773 (m-40) cc_final: 0.8465 (m110) REVERT: C 20 MET cc_start: 0.8263 (tpt) cc_final: 0.7818 (ptp) REVERT: C 21 PHE cc_start: 0.8957 (m-80) cc_final: 0.8247 (t80) REVERT: C 82 ASP cc_start: 0.8634 (m-30) cc_final: 0.7986 (p0) REVERT: C 92 PHE cc_start: 0.8157 (t80) cc_final: 0.7694 (t80) REVERT: C 95 MET cc_start: 0.8680 (tmm) cc_final: 0.8336 (tmm) REVERT: C 105 TYR cc_start: 0.7943 (m-80) cc_final: 0.7553 (m-80) REVERT: C 122 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: C 178 PHE cc_start: 0.9035 (m-10) cc_final: 0.8762 (m-10) REVERT: C 183 LYS cc_start: 0.8023 (pttm) cc_final: 0.7808 (pttm) REVERT: C 227 PHE cc_start: 0.8697 (t80) cc_final: 0.8431 (t80) REVERT: C 233 ASN cc_start: 0.8897 (m110) cc_final: 0.8373 (p0) REVERT: C 242 TYR cc_start: 0.9203 (t80) cc_final: 0.8649 (t80) REVERT: C 270 ASN cc_start: 0.8689 (m-40) cc_final: 0.8438 (m-40) REVERT: C 287 LEU cc_start: 0.2402 (OUTLIER) cc_final: 0.1917 (mt) REVERT: D 30 TRP cc_start: 0.8513 (p-90) cc_final: 0.8138 (p-90) REVERT: D 46 TYR cc_start: 0.8995 (m-10) cc_final: 0.8672 (m-10) REVERT: D 116 GLU cc_start: 0.8096 (pm20) cc_final: 0.7371 (pm20) REVERT: D 137 MET cc_start: 0.6060 (mtp) cc_final: 0.5696 (mmt) REVERT: D 154 PHE cc_start: 0.9391 (t80) cc_final: 0.8901 (t80) REVERT: D 178 PHE cc_start: 0.9332 (m-80) cc_final: 0.8723 (m-80) REVERT: D 207 LEU cc_start: 0.9439 (mm) cc_final: 0.9065 (mm) REVERT: D 210 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8627 (pp30) REVERT: D 212 ILE cc_start: 0.9643 (mt) cc_final: 0.9371 (mp) REVERT: D 213 TYR cc_start: 0.8496 (t80) cc_final: 0.8096 (t80) REVERT: D 215 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8720 (mtmm) REVERT: D 227 PHE cc_start: 0.9191 (m-80) cc_final: 0.8943 (m-80) REVERT: D 236 TYR cc_start: 0.7834 (t80) cc_final: 0.7413 (t80) REVERT: D 242 TYR cc_start: 0.8047 (t80) cc_final: 0.7417 (t80) REVERT: D 244 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8149 (pt0) REVERT: D 263 ASN cc_start: 0.8509 (p0) cc_final: 0.8132 (p0) outliers start: 65 outliers final: 38 residues processed: 606 average time/residue: 0.2806 time to fit residues: 251.4912 Evaluate side-chains 581 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 533 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 9.9990 chunk 51 optimal weight: 0.0970 chunk 88 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096710 restraints weight = 28806.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100206 restraints weight = 12215.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102371 restraints weight = 7030.126| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16299 Z= 0.127 Angle : 0.629 15.840 22004 Z= 0.326 Chirality : 0.042 0.204 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.398 145.157 2216 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.63 % Allowed : 25.03 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1928 helix: 1.24 (0.15), residues: 1143 sheet: -0.25 (0.41), residues: 144 loop : 0.30 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 124 HIS 0.024 0.001 HIS C 201 PHE 0.030 0.001 PHE D 172 TYR 0.028 0.001 TYR B 613 ARG 0.007 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 896) hydrogen bonds : angle 4.91460 ( 2616) covalent geometry : bond 0.00279 (16298) covalent geometry : angle 0.62883 (22004) Misc. bond : bond 0.00029 ( 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 623 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 578 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8155 (m-70) cc_final: 0.7923 (m-70) REVERT: A 102 ASN cc_start: 0.8875 (m-40) cc_final: 0.8513 (t0) REVERT: A 228 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8663 (mmtt) REVERT: A 266 LYS cc_start: 0.9022 (mttt) cc_final: 0.8787 (mttp) REVERT: A 286 ASP cc_start: 0.8692 (m-30) cc_final: 0.7826 (m-30) REVERT: A 344 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 355 TYR cc_start: 0.8811 (m-80) cc_final: 0.8413 (m-80) REVERT: A 362 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: A 379 SER cc_start: 0.9156 (t) cc_final: 0.8906 (t) REVERT: A 444 ASP cc_start: 0.8407 (t0) cc_final: 0.8107 (t0) REVERT: A 485 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.7611 (mtm110) REVERT: A 570 MET cc_start: 0.8844 (mtp) cc_final: 0.8554 (mtp) REVERT: A 604 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7780 (ttm110) REVERT: A 639 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: A 684 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: B 98 PHE cc_start: 0.9260 (t80) cc_final: 0.8549 (t80) REVERT: B 109 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: B 250 TYR cc_start: 0.9345 (m-80) cc_final: 0.7732 (m-80) REVERT: B 263 ASP cc_start: 0.8823 (m-30) cc_final: 0.8361 (m-30) REVERT: B 286 ASP cc_start: 0.8116 (m-30) cc_final: 0.7507 (m-30) REVERT: B 334 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8717 (ptpp) REVERT: B 355 TYR cc_start: 0.8547 (m-80) cc_final: 0.8290 (m-80) REVERT: B 357 TYR cc_start: 0.8900 (m-10) cc_final: 0.8625 (m-80) REVERT: B 362 ASP cc_start: 0.7996 (m-30) cc_final: 0.6747 (m-30) REVERT: B 379 SER cc_start: 0.9208 (t) cc_final: 0.8497 (t) REVERT: B 586 TYR cc_start: 0.8876 (m-80) cc_final: 0.8497 (m-80) REVERT: B 599 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: B 602 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 612 TYR cc_start: 0.8664 (m-80) cc_final: 0.7823 (m-80) REVERT: B 628 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8021 (mm-30) REVERT: B 655 THR cc_start: 0.9396 (m) cc_final: 0.8909 (p) REVERT: C 20 MET cc_start: 0.8074 (tpt) cc_final: 0.7314 (ptp) REVERT: C 21 PHE cc_start: 0.8972 (m-80) cc_final: 0.8236 (t80) REVERT: C 40 ASP cc_start: 0.8858 (p0) cc_final: 0.8392 (p0) REVERT: C 82 ASP cc_start: 0.8526 (m-30) cc_final: 0.7954 (p0) REVERT: C 92 PHE cc_start: 0.8007 (t80) cc_final: 0.7602 (t80) REVERT: C 95 MET cc_start: 0.8592 (tmm) cc_final: 0.8306 (tmm) REVERT: C 105 TYR cc_start: 0.8037 (m-80) cc_final: 0.7679 (m-80) REVERT: C 122 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: C 178 PHE cc_start: 0.8961 (m-10) cc_final: 0.8268 (m-10) REVERT: C 183 LYS cc_start: 0.7958 (pttm) cc_final: 0.7609 (pttm) REVERT: C 192 ASN cc_start: 0.8888 (p0) cc_final: 0.8512 (p0) REVERT: C 227 PHE cc_start: 0.8689 (t80) cc_final: 0.8315 (t80) REVERT: C 231 LEU cc_start: 0.9352 (mm) cc_final: 0.8912 (pp) REVERT: C 233 ASN cc_start: 0.8874 (m110) cc_final: 0.8575 (p0) REVERT: C 242 TYR cc_start: 0.9232 (t80) cc_final: 0.8731 (t80) REVERT: C 245 ASP cc_start: 0.9357 (t0) cc_final: 0.8754 (m-30) REVERT: C 270 ASN cc_start: 0.8734 (m-40) cc_final: 0.8491 (m-40) REVERT: C 276 TYR cc_start: 0.8004 (t80) cc_final: 0.7788 (t80) REVERT: C 287 LEU cc_start: 0.2413 (OUTLIER) cc_final: 0.1995 (mt) REVERT: D 30 TRP cc_start: 0.8596 (p-90) cc_final: 0.8056 (p-90) REVERT: D 56 MET cc_start: 0.7091 (mmm) cc_final: 0.6416 (ptp) REVERT: D 137 MET cc_start: 0.6234 (mtp) cc_final: 0.5827 (mmt) REVERT: D 154 PHE cc_start: 0.9380 (t80) cc_final: 0.8824 (t80) REVERT: D 169 TYR cc_start: 0.8650 (m-80) cc_final: 0.8210 (m-80) REVERT: D 178 PHE cc_start: 0.9327 (m-80) cc_final: 0.8873 (m-80) REVERT: D 213 TYR cc_start: 0.8489 (t80) cc_final: 0.7867 (t80) REVERT: D 236 TYR cc_start: 0.7791 (t80) cc_final: 0.7539 (t80) REVERT: D 244 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8235 (pt0) REVERT: D 263 ASN cc_start: 0.8347 (p0) cc_final: 0.7918 (p0) REVERT: D 287 LEU cc_start: 0.5912 (mp) cc_final: 0.5462 (mt) outliers start: 45 outliers final: 30 residues processed: 590 average time/residue: 0.2823 time to fit residues: 245.6208 Evaluate side-chains 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 530 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 185 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 387 GLN C 24 GLN C 25 ASN ** D 238 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 = 0.3711 r_free = 0.3711 target = 0.137682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096465 restraints weight = 29207.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099856 restraints weight = 12402.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.101999 restraints weight = 7151.828| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5880 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= 0.152 Angle : 0.656 15.416 22004 Z= 0.341 Chirality : 0.044 0.277 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.391 144.854 2216 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.15 % Allowed : 25.90 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1928 helix: 1.14 (0.15), residues: 1153 sheet: -0.50 (0.41), residues: 156 loop : 0.32 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 44 HIS 0.027 0.001 HIS C 201 PHE 0.027 0.002 PHE D 172 TYR 0.020 0.001 TYR D 22 ARG 0.007 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 896) hydrogen bonds : angle 4.98209 ( 2616) covalent geometry : bond 0.00345 (16298) covalent geometry : angle 0.65633 (22004) Misc. bond : bond 0.00033 ( 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 603 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 549 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8147 (m-70) cc_final: 0.7873 (m-70) REVERT: A 102 ASN cc_start: 0.8879 (m-40) cc_final: 0.8428 (t0) REVERT: A 228 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8693 (mmtt) REVERT: A 266 LYS cc_start: 0.9025 (mttt) cc_final: 0.8779 (mttp) REVERT: A 286 ASP cc_start: 0.8654 (m-30) cc_final: 0.7762 (m-30) REVERT: A 344 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 355 TYR cc_start: 0.8852 (m-80) cc_final: 0.8457 (m-80) REVERT: A 362 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: A 379 SER cc_start: 0.9113 (t) cc_final: 0.8855 (t) REVERT: A 406 ASP cc_start: 0.8182 (m-30) cc_final: 0.7864 (m-30) REVERT: A 485 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.7655 (mtm110) REVERT: A 570 MET cc_start: 0.8862 (mtp) cc_final: 0.8538 (mtp) REVERT: A 639 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: A 684 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: B 15 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8174 (mp0) REVERT: B 98 PHE cc_start: 0.9293 (t80) cc_final: 0.8552 (t80) REVERT: B 167 LEU cc_start: 0.9103 (mt) cc_final: 0.8587 (mp) REVERT: B 250 TYR cc_start: 0.9371 (m-80) cc_final: 0.7757 (m-80) REVERT: B 263 ASP cc_start: 0.8816 (m-30) cc_final: 0.8349 (m-30) REVERT: B 286 ASP cc_start: 0.8072 (m-30) cc_final: 0.7333 (m-30) REVERT: B 334 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8720 (ptpp) REVERT: B 342 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9346 (tt) REVERT: B 355 TYR cc_start: 0.8515 (m-80) cc_final: 0.8291 (m-80) REVERT: B 357 TYR cc_start: 0.9037 (m-10) cc_final: 0.8691 (m-80) REVERT: B 362 ASP cc_start: 0.7996 (m-30) cc_final: 0.6716 (m-30) REVERT: B 379 SER cc_start: 0.9213 (t) cc_final: 0.8571 (t) REVERT: B 586 TYR cc_start: 0.9002 (m-80) cc_final: 0.8578 (m-80) REVERT: B 599 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 602 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7601 (tm-30) REVERT: B 610 LYS cc_start: 0.8827 (tppt) cc_final: 0.8461 (tppt) REVERT: B 612 TYR cc_start: 0.8649 (m-80) cc_final: 0.7852 (m-80) REVERT: B 628 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8019 (mm-30) REVERT: B 655 THR cc_start: 0.9383 (m) cc_final: 0.8975 (p) REVERT: B 659 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7738 (mmmt) REVERT: C 20 MET cc_start: 0.7620 (tpt) cc_final: 0.7397 (ptp) REVERT: C 21 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8310 (t80) REVERT: C 24 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7758 (mm-40) REVERT: C 40 ASP cc_start: 0.9009 (p0) cc_final: 0.8235 (p0) REVERT: C 82 ASP cc_start: 0.8513 (m-30) cc_final: 0.7972 (p0) REVERT: C 92 PHE cc_start: 0.8067 (t80) cc_final: 0.7653 (t80) REVERT: C 95 MET cc_start: 0.8772 (tmm) cc_final: 0.8311 (tmm) REVERT: C 105 TYR cc_start: 0.8195 (m-80) cc_final: 0.7838 (m-80) REVERT: C 107 ASN cc_start: 0.9013 (p0) cc_final: 0.8798 (p0) REVERT: C 122 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: C 134 LYS cc_start: 0.9367 (pttt) cc_final: 0.8966 (tppt) REVERT: C 178 PHE cc_start: 0.9076 (m-10) cc_final: 0.8771 (m-10) REVERT: C 192 ASN cc_start: 0.8948 (p0) cc_final: 0.8515 (p0) REVERT: C 227 PHE cc_start: 0.8733 (t80) cc_final: 0.8393 (t80) REVERT: C 231 LEU cc_start: 0.9428 (mm) cc_final: 0.8972 (pp) REVERT: C 233 ASN cc_start: 0.8779 (m110) cc_final: 0.8458 (p0) REVERT: C 242 TYR cc_start: 0.9196 (t80) cc_final: 0.8692 (t80) REVERT: C 270 ASN cc_start: 0.8725 (m-40) cc_final: 0.8484 (m-40) REVERT: D 30 TRP cc_start: 0.8635 (p-90) cc_final: 0.8025 (p-90) REVERT: D 56 MET cc_start: 0.7277 (mmm) cc_final: 0.6431 (ptp) REVERT: D 137 MET cc_start: 0.6229 (mtp) cc_final: 0.5853 (mmt) REVERT: D 154 PHE cc_start: 0.9358 (t80) cc_final: 0.8858 (t80) REVERT: D 155 LYS cc_start: 0.9250 (mmmt) cc_final: 0.8955 (mmmm) REVERT: D 169 TYR cc_start: 0.8628 (m-80) cc_final: 0.8189 (m-80) REVERT: D 178 PHE cc_start: 0.9337 (m-80) cc_final: 0.8967 (m-80) REVERT: D 212 ILE cc_start: 0.9499 (mt) cc_final: 0.9282 (pt) REVERT: D 213 TYR cc_start: 0.8506 (t80) cc_final: 0.7969 (t80) REVERT: D 227 PHE cc_start: 0.9215 (m-80) cc_final: 0.8917 (m-80) REVERT: D 236 TYR cc_start: 0.8018 (t80) cc_final: 0.7716 (t80) REVERT: D 242 TYR cc_start: 0.7668 (t80) cc_final: 0.7161 (m-80) REVERT: D 263 ASN cc_start: 0.8295 (p0) cc_final: 0.7853 (p0) REVERT: D 287 LEU cc_start: 0.5934 (mp) cc_final: 0.5507 (mt) outliers start: 54 outliers final: 31 residues processed: 567 average time/residue: 0.2717 time to fit residues: 227.5275 Evaluate side-chains 567 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 528 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** B 131 ASN C 132 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096450 restraints weight = 28962.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099935 restraints weight = 12267.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102044 restraints weight = 7118.275| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16299 Z= 0.141 Angle : 0.677 14.885 22004 Z= 0.350 Chirality : 0.044 0.290 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.314 143.845 2216 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.98 % Allowed : 26.31 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1928 helix: 1.19 (0.15), residues: 1153 sheet: -0.48 (0.42), residues: 150 loop : 0.34 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 44 HIS 0.027 0.001 HIS C 201 PHE 0.025 0.002 PHE D 172 TYR 0.018 0.001 TYR D 22 ARG 0.008 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 896) hydrogen bonds : angle 4.96873 ( 2616) covalent geometry : bond 0.00318 (16298) covalent geometry : angle 0.67738 (22004) Misc. bond : bond 0.00018 ( 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 605 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 554 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 49 HIS cc_start: 0.8108 (m-70) cc_final: 0.7817 (m-70) REVERT: A 102 ASN cc_start: 0.8892 (m-40) cc_final: 0.8412 (t0) REVERT: A 228 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8694 (mmtt) REVERT: A 286 ASP cc_start: 0.8673 (m-30) cc_final: 0.7916 (m-30) REVERT: A 344 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 355 TYR cc_start: 0.8813 (m-80) cc_final: 0.8434 (m-80) REVERT: A 362 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: A 406 ASP cc_start: 0.8198 (m-30) cc_final: 0.7911 (m-30) REVERT: A 485 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.7570 (mtm110) REVERT: A 570 MET cc_start: 0.8865 (mtp) cc_final: 0.8538 (mtp) REVERT: A 586 TYR cc_start: 0.8973 (m-10) cc_final: 0.8340 (m-10) REVERT: A 602 GLU cc_start: 0.7713 (tt0) cc_final: 0.6617 (tt0) REVERT: A 604 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7902 (mmt90) REVERT: A 639 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: A 684 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: B 15 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8086 (mp0) REVERT: B 98 PHE cc_start: 0.9273 (t80) cc_final: 0.8474 (t80) REVERT: B 121 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8826 (tpt170) REVERT: B 167 LEU cc_start: 0.9093 (mt) cc_final: 0.8570 (mp) REVERT: B 250 TYR cc_start: 0.9345 (m-80) cc_final: 0.7735 (m-80) REVERT: B 263 ASP cc_start: 0.8809 (m-30) cc_final: 0.8329 (m-30) REVERT: B 286 ASP cc_start: 0.8069 (m-30) cc_final: 0.7342 (m-30) REVERT: B 355 TYR cc_start: 0.8509 (m-80) cc_final: 0.8294 (m-80) REVERT: B 357 TYR cc_start: 0.8968 (m-10) cc_final: 0.8658 (m-80) REVERT: B 362 ASP cc_start: 0.7983 (m-30) cc_final: 0.6757 (m-30) REVERT: B 379 SER cc_start: 0.9203 (t) cc_final: 0.8525 (t) REVERT: B 586 TYR cc_start: 0.9081 (m-80) cc_final: 0.8614 (m-80) REVERT: B 599 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: B 602 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 610 LYS cc_start: 0.8920 (tppt) cc_final: 0.8602 (tppt) REVERT: B 612 TYR cc_start: 0.8481 (m-80) cc_final: 0.7862 (m-80) REVERT: B 628 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7997 (mm-30) REVERT: B 655 THR cc_start: 0.9393 (m) cc_final: 0.9075 (p) REVERT: B 659 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7837 (mmmt) REVERT: B 688 LYS cc_start: 0.8778 (tmmt) cc_final: 0.8051 (tmmt) REVERT: C 20 MET cc_start: 0.7621 (tpt) cc_final: 0.7381 (ptp) REVERT: C 21 PHE cc_start: 0.8990 (m-80) cc_final: 0.8319 (t80) REVERT: C 24 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7882 (mm-40) REVERT: C 40 ASP cc_start: 0.9020 (p0) cc_final: 0.8156 (p0) REVERT: C 82 ASP cc_start: 0.8438 (m-30) cc_final: 0.7946 (p0) REVERT: C 92 PHE cc_start: 0.7951 (t80) cc_final: 0.7436 (t80) REVERT: C 95 MET cc_start: 0.8669 (tmm) cc_final: 0.8164 (tmm) REVERT: C 105 TYR cc_start: 0.8303 (m-80) cc_final: 0.8001 (m-80) REVERT: C 107 ASN cc_start: 0.8977 (p0) cc_final: 0.8753 (p0) REVERT: C 122 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: C 134 LYS cc_start: 0.9342 (pttt) cc_final: 0.8967 (tppt) REVERT: C 137 MET cc_start: 0.8345 (ptp) cc_final: 0.7946 (ptp) REVERT: C 178 PHE cc_start: 0.9028 (m-10) cc_final: 0.8461 (m-10) REVERT: C 192 ASN cc_start: 0.8943 (p0) cc_final: 0.8408 (p0) REVERT: C 227 PHE cc_start: 0.8730 (t80) cc_final: 0.8402 (t80) REVERT: C 231 LEU cc_start: 0.9441 (mm) cc_final: 0.8945 (pp) REVERT: C 233 ASN cc_start: 0.8977 (m110) cc_final: 0.8565 (p0) REVERT: C 242 TYR cc_start: 0.9201 (t80) cc_final: 0.8784 (t80) REVERT: C 245 ASP cc_start: 0.9356 (t0) cc_final: 0.8918 (m-30) REVERT: C 270 ASN cc_start: 0.8777 (m-40) cc_final: 0.8551 (m-40) REVERT: D 30 TRP cc_start: 0.8583 (p-90) cc_final: 0.8006 (p-90) REVERT: D 56 MET cc_start: 0.7569 (mmm) cc_final: 0.7365 (mmm) REVERT: D 137 MET cc_start: 0.6458 (mtp) cc_final: 0.6036 (mmt) REVERT: D 154 PHE cc_start: 0.9320 (t80) cc_final: 0.8820 (t80) REVERT: D 169 TYR cc_start: 0.8692 (m-80) cc_final: 0.8244 (m-80) REVERT: D 178 PHE cc_start: 0.9355 (m-80) cc_final: 0.8904 (m-80) REVERT: D 185 MET cc_start: 0.8529 (pmm) cc_final: 0.8268 (pmm) REVERT: D 213 TYR cc_start: 0.8437 (t80) cc_final: 0.7873 (t80) REVERT: D 236 TYR cc_start: 0.7908 (t80) cc_final: 0.7653 (t80) REVERT: D 246 LEU cc_start: 0.8558 (tp) cc_final: 0.8274 (mt) REVERT: D 287 LEU cc_start: 0.6025 (mp) cc_final: 0.5610 (mt) outliers start: 51 outliers final: 33 residues processed: 574 average time/residue: 0.2803 time to fit residues: 236.5121 Evaluate side-chains 571 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 532 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 122 optimal weight: 0.0050 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097133 restraints weight = 28921.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100580 restraints weight = 12156.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102668 restraints weight = 7073.156| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6222 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= 0.151 Angle : 0.692 16.936 22004 Z= 0.356 Chirality : 0.044 0.178 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.307 144.408 2216 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.92 % Allowed : 26.31 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 1928 helix: 1.12 (0.15), residues: 1157 sheet: -0.48 (0.42), residues: 148 loop : 0.36 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 30 HIS 0.029 0.001 HIS C 201 PHE 0.034 0.002 PHE D 227 TYR 0.021 0.001 TYR D 22 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 896) hydrogen bonds : angle 5.04533 ( 2616) covalent geometry : bond 0.00345 (16298) covalent geometry : angle 0.69161 (22004) Misc. bond : bond 0.00023 ( 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 593 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 543 time to evaluate : 1.789 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 15 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8266 (mm-30) REVERT: A 49 HIS cc_start: 0.8115 (m-70) cc_final: 0.7771 (m-70) REVERT: A 102 ASN cc_start: 0.8893 (m-40) cc_final: 0.8382 (t0) REVERT: A 228 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8730 (mmtt) REVERT: A 286 ASP cc_start: 0.8663 (m-30) cc_final: 0.7912 (m-30) REVERT: A 344 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 355 TYR cc_start: 0.8826 (m-80) cc_final: 0.8452 (m-80) REVERT: A 362 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: A 384 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.6383 (pm20) REVERT: A 444 ASP cc_start: 0.8177 (t0) cc_final: 0.7959 (t70) REVERT: A 485 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.7627 (mtm110) REVERT: A 570 MET cc_start: 0.8877 (mtp) cc_final: 0.8535 (mtp) REVERT: A 602 GLU cc_start: 0.7797 (tt0) cc_final: 0.6606 (tt0) REVERT: A 684 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: B 15 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8140 (mp0) REVERT: B 44 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8358 (t0) REVERT: B 98 PHE cc_start: 0.9281 (t80) cc_final: 0.8429 (t80) REVERT: B 167 LEU cc_start: 0.9110 (mt) cc_final: 0.8573 (mp) REVERT: B 250 TYR cc_start: 0.9361 (m-80) cc_final: 0.7786 (m-80) REVERT: B 263 ASP cc_start: 0.8829 (m-30) cc_final: 0.8347 (m-30) REVERT: B 286 ASP cc_start: 0.8095 (m-30) cc_final: 0.7381 (m-30) REVERT: B 357 TYR cc_start: 0.8984 (m-10) cc_final: 0.8625 (m-80) REVERT: B 362 ASP cc_start: 0.7962 (m-30) cc_final: 0.6602 (m-30) REVERT: B 379 SER cc_start: 0.9191 (t) cc_final: 0.8528 (t) REVERT: B 586 TYR cc_start: 0.9113 (m-80) cc_final: 0.8586 (m-80) REVERT: B 599 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: B 602 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 610 LYS cc_start: 0.8953 (tppt) cc_final: 0.8652 (tppt) REVERT: B 612 TYR cc_start: 0.8454 (m-80) cc_final: 0.7849 (m-80) REVERT: B 628 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8031 (mm-30) REVERT: B 655 THR cc_start: 0.9410 (m) cc_final: 0.9096 (p) REVERT: B 688 LYS cc_start: 0.8477 (tmmt) cc_final: 0.7859 (tmmt) REVERT: C 21 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8301 (t80) REVERT: C 40 ASP cc_start: 0.9015 (p0) cc_final: 0.8025 (p0) REVERT: C 82 ASP cc_start: 0.8434 (m-30) cc_final: 0.7981 (p0) REVERT: C 92 PHE cc_start: 0.7951 (t80) cc_final: 0.7468 (t80) REVERT: C 95 MET cc_start: 0.8835 (tmm) cc_final: 0.8322 (tmm) REVERT: C 96 MET cc_start: 0.7335 (mmt) cc_final: 0.7044 (mmt) REVERT: C 105 TYR cc_start: 0.8314 (m-80) cc_final: 0.7995 (m-80) REVERT: C 122 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: C 178 PHE cc_start: 0.8942 (m-10) cc_final: 0.8507 (m-10) REVERT: C 192 ASN cc_start: 0.8895 (p0) cc_final: 0.8373 (p0) REVERT: C 227 PHE cc_start: 0.8728 (t80) cc_final: 0.8415 (t80) REVERT: C 231 LEU cc_start: 0.9447 (mm) cc_final: 0.8955 (pp) REVERT: C 233 ASN cc_start: 0.8943 (m110) cc_final: 0.8531 (p0) REVERT: C 245 ASP cc_start: 0.9166 (t0) cc_final: 0.8825 (m-30) REVERT: C 270 ASN cc_start: 0.8830 (m-40) cc_final: 0.8587 (m-40) REVERT: D 30 TRP cc_start: 0.8573 (p-90) cc_final: 0.7917 (p-90) REVERT: D 56 MET cc_start: 0.7512 (mmm) cc_final: 0.7276 (mmm) REVERT: D 86 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7475 (mpt-90) REVERT: D 137 MET cc_start: 0.6420 (mtp) cc_final: 0.5950 (mmt) REVERT: D 154 PHE cc_start: 0.9386 (t80) cc_final: 0.8843 (t80) REVERT: D 169 TYR cc_start: 0.8919 (m-80) cc_final: 0.8351 (m-80) REVERT: D 178 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8923 (m-80) REVERT: D 185 MET cc_start: 0.8587 (pmm) cc_final: 0.7975 (pmm) REVERT: D 205 VAL cc_start: 0.9612 (t) cc_final: 0.9404 (p) REVERT: D 213 TYR cc_start: 0.8442 (t80) cc_final: 0.7921 (t80) REVERT: D 236 TYR cc_start: 0.7865 (t80) cc_final: 0.7603 (t80) outliers start: 50 outliers final: 32 residues processed: 561 average time/residue: 0.2806 time to fit residues: 233.2305 Evaluate side-chains 567 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 527 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 180 optimal weight: 0.0040 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 chunk 190 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.2968 ------------------------------------------------------------------------------- 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** B 131 ASN C 265 ASN D 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098882 restraints weight = 28938.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102422 restraints weight = 12157.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104586 restraints weight = 6993.553| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16299 Z= 0.134 Angle : 0.708 17.003 22004 Z= 0.362 Chirality : 0.043 0.223 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.151 141.147 2216 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.28 % Allowed : 27.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1928 helix: 1.13 (0.15), residues: 1158 sheet: 0.03 (0.44), residues: 128 loop : 0.17 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 44 HIS 0.033 0.001 HIS C 201 PHE 0.041 0.001 PHE D 227 TYR 0.021 0.001 TYR D 22 ARG 0.009 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 896) hydrogen bonds : angle 5.04072 ( 2616) covalent geometry : bond 0.00298 (16298) covalent geometry : angle 0.70771 (22004) Misc. bond : bond 0.00007 ( 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 588 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 549 time to evaluate : 1.799 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 15 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 49 HIS cc_start: 0.8093 (m-70) cc_final: 0.7742 (m-70) REVERT: A 102 ASN cc_start: 0.8942 (m-40) cc_final: 0.8411 (t0) REVERT: A 228 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8706 (mmtt) REVERT: A 250 TYR cc_start: 0.8810 (m-80) cc_final: 0.7545 (m-80) REVERT: A 259 ASN cc_start: 0.8741 (m-40) cc_final: 0.8378 (m-40) REVERT: A 286 ASP cc_start: 0.8786 (m-30) cc_final: 0.8374 (m-30) REVERT: A 321 GLU cc_start: 0.8592 (tt0) cc_final: 0.8372 (pt0) REVERT: A 344 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 355 TYR cc_start: 0.8753 (m-80) cc_final: 0.8415 (m-80) REVERT: A 362 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: A 444 ASP cc_start: 0.8126 (t0) cc_final: 0.7895 (t70) REVERT: A 485 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.7584 (mtm110) REVERT: A 493 MET cc_start: 0.9076 (tmm) cc_final: 0.8822 (tmm) REVERT: A 570 MET cc_start: 0.8845 (mtp) cc_final: 0.8555 (mtp) REVERT: A 586 TYR cc_start: 0.8713 (m-10) cc_final: 0.8161 (m-10) REVERT: A 598 MET cc_start: 0.8422 (mtp) cc_final: 0.8155 (mtp) REVERT: A 602 GLU cc_start: 0.7599 (tt0) cc_final: 0.6787 (tt0) REVERT: A 639 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: A 640 MET cc_start: 0.9115 (tpp) cc_final: 0.7628 (tpp) REVERT: B 98 PHE cc_start: 0.9240 (t80) cc_final: 0.8382 (t80) REVERT: B 121 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8835 (tpt170) REVERT: B 213 ILE cc_start: 0.8668 (mp) cc_final: 0.8333 (mt) REVERT: B 250 TYR cc_start: 0.9300 (m-80) cc_final: 0.7597 (m-80) REVERT: B 263 ASP cc_start: 0.8818 (m-30) cc_final: 0.8278 (m-30) REVERT: B 286 ASP cc_start: 0.8068 (m-30) cc_final: 0.7357 (m-30) REVERT: B 362 ASP cc_start: 0.7972 (m-30) cc_final: 0.6675 (m-30) REVERT: B 379 SER cc_start: 0.9186 (t) cc_final: 0.8357 (t) REVERT: B 586 TYR cc_start: 0.9092 (m-80) cc_final: 0.8607 (m-80) REVERT: B 599 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: B 602 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 610 LYS cc_start: 0.8973 (tppt) cc_final: 0.8662 (tppt) REVERT: B 612 TYR cc_start: 0.8418 (m-80) cc_final: 0.7838 (m-80) REVERT: B 628 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7957 (mm-30) REVERT: B 650 GLN cc_start: 0.8645 (mt0) cc_final: 0.8419 (mt0) REVERT: B 655 THR cc_start: 0.9409 (m) cc_final: 0.9147 (p) REVERT: C 21 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8317 (t80) REVERT: C 40 ASP cc_start: 0.9003 (p0) cc_final: 0.8051 (p0) REVERT: C 44 TRP cc_start: 0.7508 (t-100) cc_final: 0.7286 (t-100) REVERT: C 82 ASP cc_start: 0.8475 (m-30) cc_final: 0.8000 (p0) REVERT: C 91 ASN cc_start: 0.9094 (m-40) cc_final: 0.8818 (m-40) REVERT: C 92 PHE cc_start: 0.7998 (t80) cc_final: 0.7659 (t80) REVERT: C 95 MET cc_start: 0.8851 (tmm) cc_final: 0.8446 (tmm) REVERT: C 105 TYR cc_start: 0.8372 (m-80) cc_final: 0.8067 (m-80) REVERT: C 122 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: C 178 PHE cc_start: 0.8885 (m-10) cc_final: 0.8521 (m-10) REVERT: C 192 ASN cc_start: 0.8920 (p0) cc_final: 0.8415 (p0) REVERT: C 227 PHE cc_start: 0.8738 (t80) cc_final: 0.8424 (t80) REVERT: C 231 LEU cc_start: 0.9455 (mm) cc_final: 0.8990 (pp) REVERT: C 233 ASN cc_start: 0.8934 (m110) cc_final: 0.8608 (p0) REVERT: C 245 ASP cc_start: 0.9147 (t0) cc_final: 0.8877 (m-30) REVERT: C 270 ASN cc_start: 0.8821 (m-40) cc_final: 0.8598 (m-40) REVERT: D 30 TRP cc_start: 0.8481 (p-90) cc_final: 0.7891 (p-90) REVERT: D 46 TYR cc_start: 0.8931 (m-10) cc_final: 0.8585 (m-10) REVERT: D 56 MET cc_start: 0.7533 (mmm) cc_final: 0.7287 (mmm) REVERT: D 86 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7640 (mpt-90) REVERT: D 137 MET cc_start: 0.6515 (mtp) cc_final: 0.6021 (mmt) REVERT: D 154 PHE cc_start: 0.9367 (t80) cc_final: 0.9002 (t80) REVERT: D 169 TYR cc_start: 0.8987 (m-80) cc_final: 0.8387 (m-80) REVERT: D 177 TYR cc_start: 0.8747 (t80) cc_final: 0.8152 (t80) REVERT: D 178 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.8757 (m-80) REVERT: D 205 VAL cc_start: 0.9606 (t) cc_final: 0.9297 (p) REVERT: D 208 LEU cc_start: 0.9637 (mt) cc_final: 0.9242 (pp) REVERT: D 211 GLU cc_start: 0.9337 (tt0) cc_final: 0.9060 (tm-30) REVERT: D 213 TYR cc_start: 0.9115 (t80) cc_final: 0.8813 (t80) REVERT: D 236 TYR cc_start: 0.7828 (t80) cc_final: 0.7588 (t80) outliers start: 39 outliers final: 30 residues processed: 564 average time/residue: 0.2704 time to fit residues: 226.0244 Evaluate side-chains 557 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 520 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** B 44 ASN B 131 ASN D 28 GLN ** D 216 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096708 restraints weight = 29215.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.100181 restraints weight = 12373.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102323 restraints weight = 7169.936| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16299 Z= 0.169 Angle : 0.725 16.608 22004 Z= 0.374 Chirality : 0.045 0.220 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.227 144.878 2216 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.28 % Allowed : 27.60 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1928 helix: 1.11 (0.15), residues: 1142 sheet: -0.55 (0.42), residues: 148 loop : 0.21 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 44 HIS 0.033 0.001 HIS C 201 PHE 0.052 0.002 PHE D 227 TYR 0.031 0.001 TYR C 247 ARG 0.009 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 896) hydrogen bonds : angle 5.10251 ( 2616) covalent geometry : bond 0.00388 (16298) covalent geometry : angle 0.72494 (22004) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6469.43 seconds wall clock time: 113 minutes 46.27 seconds (6826.27 seconds total)